Was able to put all needed fasteners with reasonable success.
I went route with fasteners inside nested assemblies to keep main assembly with minimum amount of constraints, and It works. Now I can move all axis by changing value of PointDistance constraints and assembly is stable enough.
Of course now I see "Illegal storage access" much often. For example, if I'll change screw size in Nema23 assy when any axis assy is opened then 99% FreeCAD will close with this error, but if I'll do the change and only after that will open parent assembly then it will work fine. So some limitation, but not deal breaker.
Models in GitHub repository were updated. If someone want to take a look - clone repository, or download zip from: