So I tried it out and the trolls now die normally, and the spirit trolls no longer flicker. That's great!
However, I think part of the fix is still missing: polytweaks applied improved invisibility via script, rather than their claws, but now the trolls never go invisible. Now they are pretty easy to kill (as they are easier to hit and can be targeted by spells). Also, they no longer drain strength on a hit.
I have a save where there's a lone spirit troll down the hallway that I can easily test on. With your component installed, he's visible. If I uninstall it and install the polytweaks component, he's invisible, and becomes partially visible when he attacks me.
Any chance you could take a look at this?
edit: I had a look through the scripts and found this (in TROLSI01.BCS). But I don't know what to do with it as I don't know any programming.
Also it looks like the strength drain effect comes from a^spitrl.spl: