That is sort of intentional. This mod removes all armor items from the game, but it doesn’t remove their associated technologies. I suppose it could do that but I’d be hesitant about doing that in general due to prerequisites and the potential for some mods doing scripting based on them (like I do).
Ideally, for each overhaul mod out there I’d customise the tech tree and balance the Spidertron Engineer levels (and add more) manually, but I’ve not had time to do that yet and it doesn’t sound that fun to be honest, particularly as I’ve never played any of the overhaul mods myself, so balance would be tricky.
I’m open to suggestions though.