The answer is no. PNRs cannot be combined.

They can be split, but not combined.

Nor is it possible to book separate fare classes etc on the same PNR.

To be on the same PNR, you need to book identical itineraries - same flights, same fare classes, everything. The instant you want to change anything between the two (or more), separate PNRs are the only way to go.

For IRROPs protection, you can ask for them to be linked, but that only does anything if someone is handling it manually (and sees the note on the file); when the system does auto-re-bookings, it doesn't see or care about that.