Getting the grip completely under the heel pad of the left hand causes some severe deformities of alignments that I see all the time. For one the player's putter is never soled properly. The toe will always be up. Putting in this way over an extended period will create right alignment more often than not.
Getting number 3 loaded up will also get the forearms out of plane which will now have the shaft and arms out of plane and "hurt" (possibly destroy) the flying wedges.
If it feels uncomfortable lying under the thumb pad (zeroing out #3) then get the putter setting a little under the heel pad. But look, look in front of a mirror at your address postures to make certain you don't create any severe misalignments of the above.