Yea, leave it in place... stops the condensation collecting in the hood (well most of it !) dont worry about air gap, there will be plenty of gaps.. especially where cables and pipes etc go under it (I use a pair of scissors to chop slots...)
trust me leave it on.... Im having to made a whole new lid for my tank as I got sick of green algae growing on the condensation lids so I removed them... with in a month the wooden lid had warped so so so badly... its also a good percausonary thing as you never know when little finger or big ones are going to go poking around
I just thought i'd add, as I dont think it's been mentioned, it also helps keep your water temperature stable, my lid has quite big holes at the back for the lighting cable etc, so the condensation tray stops all the warm air escaping