Many will take APES and skip physics altogether, and many of those students get into top schools. Physics would be nice but I don’t think it’s make or break.
My W&L admit took zero AP STEM except APES and Calc AB if I recall and not physics at all.
As for the ‘before apply’ most Seniors take important classes during and after they apply. So Physics would be no different - than say a Senior taking Calc or pre Calc or AP English or Econ etc.