If I understand you correctly ....
You have no rom tower, so you should install the
new 3.1 chips orented the same was the 2.04 chips
were. The stick-on label doesn't really mean anything.
You are correct that the notch and dimple indicate the
front (pin one) position so install them the same as the
old chips and pay attention to the chip numbers.
If you put chip one in the chip two position it just
won't boot, I'm not sure what would happen if you turned
the chips 180 degrees and installed them.