The Good Materials innate for Engineer doesn't affect the maximum HP/FP of deployed bots whatsoever.
There was no change in their HP/FP between having the innate equipped or unequipped.
Do bots still take HP to perform actions?
Nope, not anymore, only during Overclock
It's worth noting Good Materials was changed to increase their max HP/FP. Or well, the wording of it was changed to say it does that.
As stated only Overclock causes them to lose HP for actions taken now, but GM was altered to no longer be a reduction to hp lost per action since that was removed.
I only state the potentially obvious for clarity's sake.
UPDATE: The actual issue is that Good Materials just always applies, regardless of being equipped or not. I didn't think it pertinent to double check that, but testing it now, that's the case.
I actually don't think it was ever programmed, but it has been now.
Sorry if my (additional) response was too late or unclear, but I meant that the skill did work, it just functioned as soon as points were applied rather than when the skill was added to your skill pool, hence my confusion between there being no difference with it unequipped/equipped in hp/fp (with points invested into it).
Now the skill applies when it's equipped on top of this. But for some reason the game removes the additional health this grants (I.E. 1400 goes back down to 870, though their max hp remains the same, their current hp gets cut after a round). This HP cut works in a strange way, affecting things like Malmelo, but refusing to allow their hp to go up any higher than what it got cut down to (I.E. 870 will remain at 870 despite the max HP appearing to be 1400, and percentage based heals will heal based on that maximum HP instead, though never restoring above the initial number).
TL;DR
Good Materials was just working no matter what as soon as you applied points, now it's working both when it's equipped -and- with just points in it, though has a strange interaction when you try to do both.