Can you confirm visual corruption for M30 and M36?
I am thinking Part -> Create simple copy could be a nice strategy to overcome the issue if the .fcstd file will be opened on location where your workbench isn't installed...
Yes you are right on both points.
For the M30 and M36 issue, It looks like a OpenCascade Boolean operation bug which I have no access to. To overcome this I have tweaked the dimensions of the nut's features slightly and it seems to work properly now.
Regarding your 'simplify' idea, I could not agree more. I have added a new toolbar function to the fasteners workbench. To use it, simply select all the objects you want to simplify and click the simplify button. They will appear as new "Shape" parts. You can then delete the original fastners, and the result is a simple FreeCAD file. This simplify function can work on SheetMetal parts as well.
I have updated both Git and my site with the new version.