That's an awfully contrived interpretation of that rule. There are a number of underlying assumptions that show up no-where else in any rules interaction.
We know the following things hold true in general:
-Spells that only affect willing targets fail on unwilling targets (no save).
-The subject of an ongoing Polymorph subschool spell can choose whether or not they want to have a new polymorph effect affect them.
-Baleful Polymorph dispels an ongoing polymorph effect if they fail their save.
-Other effects like spell resistance and immunities are taken into account before a save is rolled.
-If Baleful Polymorph (and by extension Polymorph Any Object) DID ignore the rule regarding choosing whether or not to be affected; that clause in the Polymorph Subschool would literally never apply in any situation ever. (that is to say that only those two spells meet the requirements for that clause to even be relevant in the first place)
So you're asking me to believe, without any support from any actual rules or precedents, that:
- For some reason being explicitly able to ignore an effect is irrelevant to whether or not that effect can affect you.
-That for some reason you roll the save BEFORE being allowed to have the option to ignore the effect (thus making that clause moot in this instance)
-That for some reason that this clause behaves differently from every other similar effect, that are all otherwise handled uniformly.
-And that, by extension of the aforementioned assumptions, an entire very straightforward clause of the polymorph sub-school rules doesn't apply at all to any part of the game.
Yeaahhhhhh.... No.