Underscanning is just overscanning, its employed alot still mainly to accomodate hidden screen edges caused by edge bevels. Without trying to sound authorative on something I know little about, a quick trip to the Wiki is in order. then there's the issue of Closed Captioning which has to be allowed for, so when showing it does not overly compress the vertical.
As for Apps that can overcome or accomodate the different outputs automatically, to me it would make little difference based on the limitations of the receiver, ie the TV.
For some it will be a compromise, whilst for a select few - heaven.
I think one of the neatest ideas was that seen on some freeview boxes where the 4:3 output matched the input 4:3 and the screen area was then filled at the side with the receivers Menu - a bit like the kind of captioning technology in Sky Sports etc. the better receivers allowed for the blanking out of the text area whilst watching a film.
There are a multitude of scanning standards based around the old terrestial Tv formats - IE, NSTC, PAL, SECAM, where those areas whilst adopting a true 1080HD at 16:9 almost universally, have, for whatever reasons utilised many different formats at the lesser 720p end of the spectrum. since it is touches on and supports this discussion I have taken the liberty of including this link;
http://en.wikipedia.org/wiki/Digital_television
Confusion abounds, and Apple as ever, as with so many others, is caught trying to cater for diverse standards with a device that it hopes can be used universally. Maybe in time - but in the meantime, compromise - may well be the order of the day.