1) You can MFU bookings (BA sectors only) which contain non-BA flights now, yes. Has to be done offline though so you will need to call them.

2) What you earn on the shorthaul leg will be irrelevant as far as MFU/no MFU goes, as it will depend on the base fare. However, for a WT+ base fare on a BA codeshare for the EI leg, it should book into Y if it's anything like BA's own connections ex-EU for example. If it's under the codeshare you should get the minimum BA miles and TPs (20 per leg) as if it was a BA flight. If it's an EI code, you'll just get the miles (no TPs).