Honestly there seem to be very few downsides to applying. If you don't like the job you're offered you don't have to take it (in fact i think you only apply to jobs you want right?). Even if you were completely neutral about the rotations, its an extra chance to get into the deanery you want, so just apply. In many cases the rotations are in fact very preferable, with AFP jobs sometimes being the only jobs in a deanery with both years in the most popular location.
There is also this perception, whether correct or not, that if you are in AFP you are just better and are more deserving of audit and research opportunities. I know of SHOs who have missed out on career-specific opportunities just because the academic FY1 heard about it and wanted it instead (and then did a terrible job!).
If in doubt, just apply.