When you start up the Pi-Hole if you have a lot of lists, you get a lot of noise from malformed lines. It seems that the Pi-hole preens the list anyway, it would be cool if it had an option to create a new list that leaves out the malformed lines. This sounds like it would be pretty easy to do.
Where do you see a lot of noise?
gravity.db since v5.0 it is pretty easy to get a (deduped) list of all domains pihole has in it's database collected from all adlists:
sqlite3 /etc/pihole/gravity.db "select distinct(domain) from gravity;"
P.S. Best approach would be to use lists with less noise from malformed lines