I always thought that the Mach3 install was rather simple {i.e. it did not install any DLL's in any other directories other than the C:\Mach3 folder, and it did not fiddle with the registry {much}}
hence I am surprised that it would cause problems with the overall installation of windows or allowing it to boot.
Threading on Mach3 lathe or turn I believe was always complex / problematic because of its use of a single pulse index (only) for spindle timing.
Hence UCCNC should be better allowing for the use of a proper multi-pulse per rev encoder.
The problem with mach3 and mach 4 is that it is just the planner software and it does not provide any hardware so there will always be hardware and software incompatibilities because of having 1 software developer (artsoft) and many hardware providers. Sure you have access to the api (as long as you have signed the NDA) but details of what changes between versions is always sketchy.
Hence uccnc is miles better as you have 1 hardware and software developer and they should be able to manage and control their code to just work with their hardware. Problem is you ae still reliant on whatever access they give you to the hardware or software and whatever features they see as being beneficial or developable.
Centroid is another hardware and software provided as an integrated system. I looked briefly at their system many years ago now. I thought it was rather expensive given you buy the hardware and then you have to unlock the software functionality. Also you just unlock it to run...... I don't believe you can modify anything about it (other than m-codes) i.e. no screenset editing, and no plugins etc etc. You get it as it is and it works as it is, like it or lump it. you are also limited to the hardware.
There are a few companies listed here who may be able to offer alternatives.
https://mellowpine.com/cnc/best-cnc-controllers/
There was a Canadian motion controller manufacturer that looked promising a while ago, I just cannot find or remember their name. They seemed similar to the Warp9 ESS, but did the software package too. I think they did turn.... {its going to bug me now}
Again the problem is turn seems to be quite limited in who can do it or wants to provide it because it seems such a small market compared to all the other linear axis (Cartesian plane?) motion machines (routers, mills, 3 d printers, laser cutters etc etc).