Based on the US situation, there will be a few stages. First, a period of time where you get more Tier Points booking the codeshare as the partner. Then, BA will notice this is going on, and get Avios Group to fix the discrepancy. Then, for a while, MMB and the Calculator will be wrong, until BA get around to fixing it. As Cymro says, during that period the Exec Club is likely to honour your expectation. After they fix ba.com though, they won't be flexible anymore, apart from people who claim they relied on ba.com info to make their tier.

I imagine we are still at stage one, as based on the US scenario, it took months for AGL to change the unfair advantage to booking codeshares as the partner instead of BA.