I agree with this point. Overall, this patch is really awesome and I love it, but these changes are negatives in my opinion. They change mechanics in the game that whether you like them or not, you are forced to contend with. The idea of the setup being taken out is kind of in this line, but it's really only relevant for a couple difficult-to-unlock jobs like Mime, Calc, etc. Even so, you're forced to contend with either getting throwaway soldiers and slooowly accruing spillover JP for these unlocks to keep your units at a low level, or forced to contend with the issue of getting higher leveled and dealing with riskier random encounters just to get the job unlocked.
Changing the availability of an item (Rubber Shoes) or a basic mechanic (critical hits) might be adjusting an issue that could use tweaking, but I feel like it ultimately affects the authenticity of the run. It would be like changing Kimahri's Thrust Kick in FFX to actually inflict Eject, or fixing Steiner's Thunder Slash and Iai Strike in IX. At that point, it's not a far jump to do things like adjust the Sanctuary Keeper's poison resistance to allow an easier infliction with back-to-back Bad Breaths in a Kimahri SCC, or nerfing the instant death rate of Anima's Pain at Macalania. Of course, those are extreme and drastic examples, but it's a slippery slope.
I think I'll check this patch out for SCC runs that aren't normally available for the player (Assassin, Ultima Demon, etc), if that's even an option. But I feel the changes that alter mechanics in any way affect the legitimacy of the run.