Hi Cloudfarm.
I tried one with 18650's and with a proper lipo.
Neither was much of a success as the MKR seems to lack any proper deep sleep.
Battery life was pretty poor with both type of battery but they do work.
if you could turn off the onboard LED's and the WiFi properly I am sure it would be so much better.
If its for a remote use app then maybe adding solar charging to the batteries would help quite a bit.