You are most likely correct: the safest mod of all is probably, as you say, a Puck-style 4-batt boxmod with either 4x '1.5v' main street rechargeable AA cells for 4.8 - 5v or 3 cells and a dummy cell for 3.6 - 3.8v. Variable voltage as well :-)
As most know, rechargeable AAs are 1.2v in reality, not 1.5v.
But the question the battery section is supposed to address is: which batt in a standard mod is going to be the safest bet. The answer is, the one least likely to blow up in your face no matter what goes wrong. There is only one answer to that question, and for a nominal 3.7v mod it's an li-mn cell (IMR).
However we could add a section with your suggestion because you are exactly right, IMO.