Let me preface this by saying that I by no means represent the majority opinion (if there is one right now), but will try to give you what insight I have. If I leave something out or misstate, I'm sure some kind soul will enlighten me...
The populations aren't lasting long due to the invasions as you correctly surmised. When selecting a harvesting square, the general trend has been as far from the front lines as possible to prolong its life. Selecting which monsters to populate has stemmed mostly from requests made on this thread or in chat. Because of the typical short life of these squares, populating a monster for a personal need has not seemed to create any dissent. I might add, when you do pop it, collect what you need in a timely manner, some squares have lasted only a few days.
Aside from that, the squares (especially those near the front lines) get wiped out very often, so 1st releases are abundant. Hope this helps, and happy dropping
--Cal