Keep a couple things in mind:
First, at boiling temperatures, your wort takes up a little more space than it does at pitching temps. It's not a ton more space, but if it looks like 6 gallons at boiling temps, it's probably closer to 5.75.
Second, boiling longer is definitely going to throw off your hop profile. I don't think it'll impact your bittering (60 minute addition) hops very much, but anything from 30 minutes in will definitely be impacted.
In general, if I'm at the end of my boil when I notice that my volume is high, I just take that high volume and cut any losses.
Take good notes over your first several brews, pay very close attention to details like your boil off rate, gravity numbers, etc. The gravity numbers, if they are consitently high or low, will help you start to identify if you need to adjust recipes to include more or less grist. Knowing your boil off rate will help you figure out how much water you need to start with, and will help you to recognize if your volume is high before you ever add any hops - which would be the ideal time to make corrections. If you know then that you'll need to extend your boil to get rid of an extra half gallon, and you know it takes you 20 minutes to boil off that half gallon, you'll know to boil for 20 minutes before you add hops and start any of your timers, etc.