Why won't my iPhone Apps appear in iTunes 12.5.5 on El Cap?
WOAH I did not expect to be answering my own question so fast.  But in case anyone else ever runs into this, here is what just fixed it for me.

I had an old iPhone 4s laying around (iOS 8.x) so decided to see if it would sync.  Hooked it up and sure enough, no problem... apps came over, etc.  Plugged my iPhone SE back in (in addition to the 4s still connected), selected the SE, and lo &amp; behold - all my apps show up.  I can't explain it as they were never transferred to the computer... but there are there and I can access the file I needed.  Very strange!