While it is true that the authority of the Colleges technically derives from the emperor, it should be noted that the power of the Colleges comes from them being well magicians. How many beastmen o(r Sigmarite flagellates) can one Bright wizard lord incinerate if they so choose? A lot. Power must be considered in terms of what the Colleges can do, subtle and overt, not just in terms of who has the most social influence by tradition.
Except we're not talking about power in the literal "I have Magic and can do stuff with it" sense alone are we? I'm discussing the social and political pressures exerted on the college that Magnus deliberately inflicted on the Colleges. The balance of power is very delicate, and disrupting it with blatant moves can cause the whole system to crumble. Notice the wording of some of these articles of example:
1. The first obedience of every Magister must be to the ideals and laws of Sigmar's Holy Empire of which these Articles form a part; then to he who is rightfully elected Emperor of Sigmar's Holy Empire; then to the Supreme Patriarch of the Colleges of Magic; then to the laws and ideals of their Order; then to the Patriarch of their Order; then to the authorities that each Magister may be required to serve in the course of his duties; then to other superiors within their Orders.
2. No Magister may obstruct in malice or for financial or political gain the rulings of the Emperor, nor may they seek to overthrow him for these reasons.
3. Every Magister of said Colleges must adhere to the laws of Sigmar's Holy Empire, regardless of the province, region, or city-state, just as any loyal citizen must, except that the Magisters alone shall be permitted to study magic and perform such spells for the good of the Empire.
The wording is important here because the actions of the colleges are laid out here. The first loyalty is to the laws and ideals of the Empire, including the Articles, THEN the Emperor, then the Supreme Patriarch, then the laws of their order, then the patriarch, then the authorities, then the Order. They may not obstruct in malice or financial or political gain the rulings of the Emperor, which is a very broad statement, and they must followed the laws. But there's more:
6. No Magister may cast a spell or enchantment outside of the theatre of war and in public view without first being requested to by the Emperor, the Electors of Sigmar's Holy Empire, or another legitimate employer as defined by the Articles of this document. All spells and enchantments cast without these permission may only be done so with and for demonstrably good reason.
8. The Colleges must respond favourably to any reasonable request for specific service from any Elector of Sigmar's Holy Empire.
No Magister may cast spells in public outside of war without permission from the Emperor, Electors or a legitimate employer, you can skirt around this rule by not performing magic in the public eye, but you must also skirt around other laws I will mention soon. Also notice the very careful wording of Article 8. The Colleges may not obstruct the rulings of the Emperor, but no such thing is stated for the Electors, and article 8 simply states that you must "Respond favorably" to the "reasonable requests" of an Elector. There's a clear gap here where it's made clear that the Emperor holds a great degree of power over the College and they can't mess with him unless it's for the good of the Empire, but no such thing applies to the Electors. "Favorable Response" can be just a "yup I heard your message, but I'm busy right now".
9. The Colleges must be ready to render service to the armies of the Emperor and the Electors of the Empire upon request, unless such service aids in the seceding of an Imperial province from the Empire, or unless such service is intended to cause overt harm to the Electoral System, or to the authority of the Emperor who resides upon Sigmar's Throne, or to the unity of purpose and identity that marks Sigmar's Holy Empire, as indeed it was so sorely afflicted throughout the dark centuries of the False Emperors.
Then there's this article, which is honestly kind of blatant. The colleges must be ready to render service to the armies "unless such service aids in the seceding of an Imperial Province, cause
overt harm to the
Electoral System, or to the authority of the
Emperor who resides upon Sigmar's Throne, or to the unity of purpose and identity that marks Sigmar's Empire". There are rules that explicitly disallow military involvement of the Magisters in very specific circumstances, and nearly all of them reinforce the Emperor's control over the Empire.
12. Magisters are permitted to pursue agreements of employment with any persons or organisations: civil and religious, public and private, noble and mercantile, providing their employers are not enemies of Sigmar's Holy Empire or the people and that will not lead to the breaking of any of these Articles.
This is simple, Magisters are not allowed to be employed by enemies of the Empire or by someone that would lead to them breaking any of these articles.
15. All Magisters are required to exert themselves to seek out and counter such destructive and anti-Imperial machinations, practices, peoples, and creatures that are beyond the means of civil authorities and Sigmar's Templars to counter, but yet still serve the Daemon Gods or advance the corruption of Imperial citizens through any sorcerous or infernal means. This shall be the prime concern and purpose of the Colleges, their Orders and the Magisters belonging to them, and to fail in this duty is to render void all the Articles of this document and make obsolete their permission to practise arcane arts without hindrance.
And here is the kicker, the big big BIG article. This is what Regimand used to skirt around the Articles of Imperial Magic when he assassinated the Empress. Regimand did obstruct the government of the Empire by killing the Empress and the unborn heir to the Empire, but Article 2 says "may not obstruct the rule of the Empire in
malice or financial and political gain" and article 15 here explicitly says that the articles are rendered null and void if the Magisters fail in their authority to counter "anti-imperial machinations, practices, peoples and creatures that are beyond the means of civil authorities and Sigmar's Templars to counter".
The Colleges have a lot of power yes, but all that power is useless if they violate the articles in a way that could be directly pointed to as a way to disrupt them. Except, there's a lot of leeway in the articles! The thing is, the majority of that leeway is in the hands of the Emperor. Notice how many of these articles put the Emperor's rule above the Electors in an undeniable way. Even Article 9 says that you may not render aid if it assists in "overt harm to the electoral system". Overt is the operative word here, so if the Emperor decided he wanted a magister to do something questionable, Article 1 says their loyalty is first to the law and articles, then to the Emperor, and there's nothing in the Articles that says they can't mess with an Elector. No wonder the Electors would be angry at the power the Emperor holds with the Colleges. On the other hand, it also means the Colleges have to make peace with the Emperor unles they are such a menace to the unity of the Empire that they would tear it apart, anything short of that they can make do with.