Part of it I think is just a lot of the crafting details and research and development in general being only talked about broadly now or having it done in the background (duplicates). For Waste Not, at this point most material he can just transmute and there are cases where the 50% chance thing isn't something he wants to use if what he's working on is complex and dangerous especially if it's something like new experimental magitech or exotic matter/energy research/applications.
IIRC, it was due to that perk being limited to machinery and there being diminishing returns since to repeat hybridize you need to actually be able to understand the resulting hybridized product which often is or becomes incomprehensible due to the amount of fiat involved in making the hybrization work. Also, hybridizing is already being done with stuff but the results are more general buffs via stacking existing capabilities (not mixing to output/create new unique ones).
I'd suggest a reread of the two chapters since a lot of things can be missed during the first reading as well as some of the
WoG in the AO3 comments.
Like others have said, Joe plans for it to be a complete stomp. He's gonna counter whatever they throw around and with the level of prep including surveillance, Joe isn't gonna let things like hostage taking to succeed or even take place (in Brockton at least since I expect the Nine to have hostages from outside the city).
All the reasons from before on why he doesn't launch an attack still stand. You have to remember that there are national and international consequences. The ripples will affect hundreds of thousands at least. The reason he doesn't just drone army/nuke the Nine is because of the fallout. If he goes after those with kill orders, then other groups that have kill orders or highly contentious legal standings are gonna panic and do desperate things to prepare for the expecting conflict. Joe can see the scale of this especially due to the alien/inhuman perspective and knowledge he has which is why we also read his thoughts on why he's accepted this course of action as it is one that minimizes death.
He understands that getting all these groups around the globe panicked all at once is not a smart thing. I see preemptively and unexpectedly attacking the Nine in the way some have suggest as basically putting Joe on a clock of escalating incidents around the globe of panicked and desperate groups wrecking havoc while pillaging for resources, gathering territory, securing leverage, recruiting/conscripting people, etc. Not to mention all the other groups that'd react badly such as governments and precogs and thinkers including the Simurgh. The way Joe plans to do it will avoid that by maintaining the balance and it'll give him more control of the response especially when he does eventually decide to act outside the city and expand his influence and clearly go against the mercenary image/contract-bound expectations. It's also great politically due to the controlled framing, strong justification, powerful show of force, and goodwill that'd be earned from defending the city again, this time from the Nine.
Joe wants to cut off any chance of the Nine getting away. He wants a guaranteed victory. It was mentioned in the previous chapter how there were a lot of unknowns/uncertain factors such as the sensing/detection abilities (Crawler, Shatterbird, unknown new members) or tech/creations (Mannequin, Bonesaw, also remember the parahuman disappearances Survey mentioned) of the Nine. The Siberian's unstoppable force and immovable object thing is no joke especially with how it can be shared and could combo with stuff. That alone would give worry for an avenue of escape especially since Joe doesn't know about the specific weakness of Manton being the Master. Plus there's Jack's power which is another wildcard to Joe as well as any other prep the Nine have. Anyway, these factors are why Joe is basically preparing a mouse trap.
'and remember the training' or 'don't forget the training'
...[re-reads Chapter 38]...
