It's because of injuries.
Take the eagles for instance. Let's say Fletcher Cox gets hurt week 1. It's a hamstring, bad enough that he can't play week 2, but he should be back week 3 or 4. Not bad enough for IR.
If all 53 were active, they'd have to play a man short, and would be at some level of disadvantage against us week 2, assuming all 53 of ours were healthy. Essentially they'd be playing 52 on 53.
With the 45 man game day rosters, you can just make Cox inactive for a game or two and it is still 45 on 45.
It's supposed to help make the rosters stay even in case of injuries.