This has been an issue for every jointly shared airlines trunk routes (e.g. CDG-AMS on AF-KL, FRA-ZRH on LH-LX, etc) as well as JVs for that matter) and I guess that there is no perfect way around it.

As you point out, from a route-specific point of you, it would seem to make sense to harmonise the product as its heterogeneity is frustrating for customers.

But of course, if you do that, you simply "displace" the product heterogeneity at a network level with customers being equally upset that they got free food and drink on their MAD-LHR and that now that they flying an eve longer MAD-FRA they are being asked to pay and how come. And conversely, imagine that they do the same in C where in my view, the IB product is significantly better, I can easily imagine people complaining that they received a nice full hot meal at 10am or 3pm on their 2h30 LHR-MAD but are only getting a silly afternoon tea or "brunch" snack type meal on LHR-HEL which is nearly an hour longer.

And of course, this assumes the not at all obvious notion that it would be harmonised on the higher offering (assuming this can actually be defined) while it could be harmonised on a "medium" or "low" value instead. Indeed, is the idea that in Y, you would get free food and full bar (BA) but also seat assignments for OWE/OWS on all fares without HBO exception? And in C do you get hot meals throughout the day as well as Sherry and Spanish liqueurs (IB), but also Champagne (BA) and both herbal tea collections?

And if it is indeed harmonised upwards, who will be picking up the bill(s)?

To my knowledge, ultimately all jointly-owned airline groups ended up choosing to keep network homogeneity rather than focus on route homogeneity with the exception of AF-KL introducing premium economy on all CDG-AMS flights for a relatively short period of time but arguably that was not a product harmonisation but mostly an attempt to provide of all AF's three travel classes on all CDG-AMS flights. I doubt that BA-IB will do more and if they ever did, I would imagine that it would be in the form of piloting any attempt to worsen the Y product on their MAD route.

PS: as a footnote, the BA arrangement is absurdly complex with the mix of codeshared and leased IB flights and I can understand how many passengers, let alone non-frequent ones - would be frankly confused.