I recently bought with AC on the phone a Z fare ticket to LIS through LHR and on to another Portuguese destination. LHR to LIS, TAP flight, AC codeshare. Continuation, just TAP, AC does not codeshare. Same on the way back.

I don't recall if I initially bothered about seats. This was coordinated with an Aeroplan reward for my wife so my first concern was having both on the same flights. But anyway, no problem getting seats on AC obviously. The Aeroplan people had no problem giving me the TAP locator. However when calling AC to ask same question for my ticket, they ended up giving my wife's locator on AC... (Which had been cross-referenced.)

Anyway, I phone TAP. They were nice, found my wife's reward, no problem assigning her seats on all four TAP legs. They found my locator and gave it to me. Had no problem assigning me seats with my wife on the non-AC codeshared legs.

Could not allocate me seats on the AC flights operated by TAP however (between LIS and LHR). I phone AC again, and after some time, they did find a way to assign me seats next to my wife.

Morale of the story: YMMV. Sometimes only the operating airline can allocate, sometime only the marketing one. OTOH agents may be under pressure to deal with x calls per hour and they may try to get rid of you as quickly as they can. Easier to claim they cannot than fiddling around, talk to their boss, and resolve.