My primary cover has allen bolts, the primary inspection cover has countersunk screws with allen key. But the clutch inspection cover has torx. Has anyone considered replacing the clutch cover screws with allen keys? I can't see the reason for all the different types.

replaced mine, those torx bits are soft as cheese. Replaced with the same pitch/length in allen head and all fine.

Joker machine have the bolts for sure, but any fastner shop can sort it for cheaper.

Same here, no harm at all on replacing them.  Just be careful about over-tightening the new bolts as its easy to strip the thread out of the primary cover.