Most of the stuff I've read about over filling or the dangers of over filling a gear box or a differential are related to excess foaming of the lubricating oil. If the original design says to fill it on the level using the fill to spill method then I'd stick with that.

Most differentials have a breather pipe on the top that often gets clogged - if this is clogged up and you've over filled the diff then there is a possibility that if the oil expands and / or foams excess pressure builds up - this could cause seals to fail.

My advice is to not think too much about it. Do what the manual says. Don't over fill. You've just put in some lovely new life blood (oil) - you've done the best you can.