I think you're seeing a conspiracy where none exists. Especially in summer, VY operates a lot of IB's flights, and I really can't imagine there is anyone at IB who would expend that kind of effort over something like this.

At the end of the day you're talking about a flight of about an hour, where the only difference between J and Y would have been a tiny snack and a seat at the front of the cabin. If you're booked in the highest fare class on the VY flight you should be given a duo seat anyway, though you may need to ask when you get to Madrid if you aren't able to choose it online beforehand.

Vueling is a great airline, with new planes and a friendly young crew. The duo seats (aka Vueling Business) are the first three rows with the middle blocked, so pretty much the same as any other European business class minus the snack (you can buy on board a really nice sandwich for about 4€).

Tip (speaking in general to those not used to dealing with Spanish companies): when asking for your duo seats in Madrid, be nice. Neither the person on the phone nor the person at the transfer desk will be the one who canceled your flight, there is nothing they can do about that, and they have no reason or motivation to do anything but hand you a boarding pass. A smile and a "I wonder if you can help me with my problem" will get you a lot further than stamping your feet and demanding satisfaction.