I'm guessing this doesn't work with Mods which make different versions of the steam engine?

I am running bob's mods and it doesn't seem to do anything when pressing the hot keys, not even a message, and i have Mk2 Steam engines only.

It should work, unless the steam engine is not a type=steam engine.
It goes through every type of steam engines and copies it. I have Dytech on my playthough and it adds 4 additional tiers, and these work with it...

I just tested it, and It worked fine over here, do you have any other mods? maybe something else in your list makes it not work

Think it would work with Youki's steam engines as well?

It should work fine, it makes no mayor changes except copy it.
The only issue is the name, as it would be called something like "GP-youki-steam-engine-mk2-primary" haha. I could see what youki calls their steam engines and add them on the next version with more localization names