I have a similar decision to make. Here's my thought process though. I add ingredients for a 5 gallon batch but add slightly less water or boil off more than I thought but it's only water I lose so now the beer is more concentrated than it should be. If watered down beer is a concern why don't we use 5 gallons worth of ingredients then only brew 4 gallons making it stronger?
Obviously I don't know because I'm a noob in every sense of the word, just sayin', that's all.
So I boiled to 5 gallons but left a half gallon in the boil pot. (Really should just take the whole volume to primary in future.) Now I have a little over 4.5 in primary and I need to decide whether to top off in secondary, especially since I will end up leaving behind even more volume. Shouldn't I worry about too much airspace in secondary? My brew book says to top off into the neck.