I kind of have one or two theories as to where the "super prototype" trope came from, at least from fiction/anime specific.
One is the belief that "super prototypes" exist to test and demonstrate multiple new systems at the same time in order to test these systems
concurrently from a cost-saving standpoint, but these systems had always been intended to be installed on separate platforms in actual combat as installing all of these systems on a single, mass-produced platform would be cost-prohibitive or other practical factors may interfere. Gundam and maybe a few other "real mecha" series seems to be the most likely place to encounter this rationale, but it's a bit problematic from a realism standpoint as it works 180-against practical realities - it's usually easier and more cost-effective to test systems individually, and once they're ironed out production scales make them more practical to install a bunch at a time on a single platform.
The other theory is that the "super prototype"
does represent a hoped-for production model, but a lot of the features get "drummed-out" and "dumbed-down" from the actual production version due to cost considerations. This actually
is realistic; in fact it happens almost all the time so there are at least a few real examples. Two that immediately come to mind are the YF-22 - it at least promised a whole bunch of stuff like dual proto-DAS-like IRST sensors on the wingroots and immediate AIM-9X compatibility (in fact the shape of AIM-9X is mostly dictated by the need to fit two in the F-22's side bays) that are either being very slowly implemented or completely cancelled on the production F-22 due to cost considerations. Another is DDG-1000 Zumwalt - which, again, at least on paper was going to have a whole bunch of fantastic capability such as true, SPY-1-like (actually superior) BMD capability and such, that ended up being removed from the actual vessels - but on top of that, with only three being produced they still come off as super-prototypes compared to the DDG-51 Flight III Burkes that are being produced instead. If you're looking for the best dictionary picture of a real-life super prototype, there you go. You've also got numerous Abrams prototypes and test vehicles equipped with what could still be considered semi-exotic technology such as 140mm smoothbore guns and completely automated turrets that never made it on production vehicles because the technology was either too impractical for that time or too expensive.
The final theory is that a "super prototype" isn't so much a prototype per se but just a single unit meant to be so elite and capable the exorbitant cost justifies itself in the hands of an equally elite pilot such that the two together can win the war single-handedly. This tends to be common for obvious narrative reasons, but again I guess the F-22 or B-2 kind of ends up being a close approximation of a real-life example.
For starters (and a given definition of success,) the Me-163 comes to mind. Considering the absolute insanity that involves putting guns on two very dodgy fuel tanks and a rocket motor, the fact they didn't all up and explode on the runway is success.
I don't know if that really qualifies since there were attempts made to produce the Me-163 in serial number and they managed to build quite a few. Plus...it really wasn't that "super."
Another one would be the Monitor and the Virginia at the battle of Hampton Roads. Both ironclad boats and steamships in their virgin battles, neither one failed and both succeeded to prove wooden ships outdated.
That is more appropriate, although most of their features were quickly implemented into successive ships, especially since the USN got to serial-producing turreted monitors (which of course eventually evolved into super-dreadnought battleships).
Last, I'll mention the classic prototype Devices- Little Boy and Fat Man; both of which themselves were different prototypes of the same weapon.
*shrug*? I guess? In terms of being prototypes of "the same weapon," Fat Man was a prototype implosion fission device while Little Boy was a prototype gun-type fission device. The gun-types were easier to work out so most early-generation nuclear weapons were of that type but the US quickly perfected the implosion fission bomb which quickly became the standard. Fat Man was more representative of the typical serial-produced nuclear fission bomb until being replaced by miniaturized (in comparison, so they can be loaded up onto virtually any combat aircraft in the inventory) thermonuclear bombs.
Now, Tzar Bomba, yeah. You might even argue that's a real example of at least two out of the three archetype theories I listed, if not all three.
