Yes, it's definitely a problem. It's why I very hurriedly ended my comments by saying you'll have to be very careful about the distribution of local versus the regional list seats, because you'll get at least as much if not greater distortion of the number of seats won by a party that's favoured by AV at the front end. For example, if one said that the law reform commission, without recommending AV as the way to vote on the local side, just first past the post for the local elections, recommended 65:35, or roughly two-thirds and one-third, if you kept that proportion and went to AV, it wouldn't be good enough. You'd have to at least go down to 60% in order to account for that extra distortion, for the reasons that you're saying.
I'm offering it out there as a position that would still have to be fought for. People would still have to ask what is it about AV, other than what I'm calling relatively unclear and not entirely accurate claims about majoritarianism, that people think is fixing something? If that case is made, and somebody wants to go in that direction, you can still build it into MMP. That's really my only point. It's not the first place I would go, because I think it makes the proportionality side harder to achieve.