After the third checkpoint in Canyon, there's an optional upgrade for the x-transformer, do you need it and what does it do?

As far as I know, it just increases your health/defense. There's another one in Sewers, and they stack. Not sure how much they affect the speedrun - they don't take that much time to grab, but off the top of my head I can't think of any specific mid-to-late game scenarios where having more health would considerably speed things up. Maybe for detonating those walker-mines on Zondag 1? Of course, you'll want both if you're planning on doing any IL runs.

For what it's worth, I grabbed both of them in my original 1:20 run, and when I routed my 1:12 run I decided to skip them since they didn't seem all that necessary.