It's possible that it's just part of the way it's set up.
Our Mazda has always had rather "spongy" brakes and it's been carefully bled etc. They work absolutely fine, just feel a bit spongy and we've never had any air come out.
Our other Japanese cars (Toyota's) have felt similar. Don't know if it's a Honda trait as well.
Good luck with tracking it down and sorting it out.