VP959,
you may be correct for microlights under the BMAA authority, but I doubt it. Certainly this is not correct for any under PFA authority.
Yes, the owner can work on an engine on a PFA aircraft, but their work has to be signed off by a PFA inspector. As does any work on a PFA aircraft, except similar things that you can do as "pilot Maintenance" on a C of A aircraft. Also if your rebuild includes splitting the crankcase, then your PFA inspector has to get a written approval from PFA engineering to inspect and sign off this work. This approval is required for every individual engine.
I would guess that similar rules apply for BMAA aircraft, so TURIN, I suggest you contact the BMAA and ask them.