If so, how bad is it just to edit perltidy's output yourself to fix these cases?
As I understand it, the ideal is to use Perltidy quite often, as one part of the edit cycle, cleaning up any unintentional goofs and restoring to the 'standard' formatting. Perltidy is not a one-time or once-a-month thing, rather it is supposed to be done at least before each time you check your changes back into the repository.
So you shouldn't have to clean up after the cleaner-upper. Indeed, it is this problem that has so far kept me from using Perltidy as intended.