That's not correct in my experience. I think it may be possible to exclude
IMAP accounts from filtering altogether, but if you're filtering them I'm
pretty sure it doesn't matter how you check the mailbox.
Filters don't operate on the basis of which mailbox the messages are in.
If the IMAP account were a different account than the account being
checked via POP, there would be a couple of ways to do that, but most of
them are eliminated by the fact that just about everything about the
message is going to be the same regardless of whether it is downloaded via
POP or IMAP.
If the POP personality is not the *** personality, you could have
your filters exclude messages based on the personality. (POP personalities
other than " *** " have the x-personality header, which can be looked
at by filters. Since neither *** nor IMAP accounts have it, you can't
distinguish a *** POP personality from an IMAP personality that way.)
You could also check to see whether any of the headers added by the server
end up being different depending on whether you've accessed the account
via POP or IMAP. (Open the same message downloaded each way and use the
BLahBlahBlah button to look at the full headers.)
That sounds like you'd want to use an "intersects addressbook" filter
condition to do the filtering, but first you're going to have to figure
out how to exclude the messages downloaded via POP.