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All that being said, might it be easier to take an approach from the other side.
Considering your very wishful, clingy and blatantly abusive of the DM's patience and good manners take on invisibility+stealth:
I just hope he says fine, have it your way. And then next day you get ambushed by 3 ogres with invisibility cast on them with 1 rank in Stealth(obviously stealthing while invisible). Good luck with that Perception 40+ DC.
As ShadowcatX mentioned, we are humans, so let's use our head a bit before making ludicrous assumptions that momentarily favor our PCs.
I don't see any mentions of the bonus to stealth mentioned in various places stack(unlike precise statements of DR, AC stacking for example).
Invisibility is just a spell that gives you the invisible status. For all lazybones' convenience, they just doubled their +20/40 to stealth text, to make sure that people with invisible don't forget that.
NOW, the big part: had the boss cast See Invisibility , you would be treated as visible, so straight Stealth check vs. Perception check, no bonus from Invisibility. Your case : 23 Stealth vs. whatever total Perception he had.
This may have been a problem of lack of reasoning abilities, or meek character, or something else, but for all purposes and intents, See Invisibility TOTALLY counters Invisibility(consider having ONLY this 2 spells cast, to keep it simple).
Any other way around is just you pushing the DM to something not RAI(and somewhat arguably RAW) and into the "I WIN" button territory. And remember, for every Invisibility you have, he can cast 10 and handwave the sudden surge of spellcasters. Are you sure you want an arms race?
Does it matter that much ? You said the fight ended without much loss regardless, why stir the bee's nest now ? Learn to accept DM decisions without crying "foul" on every corner.
PS. To address your "moving on"
Invisibility grants a static +20 to Stealth checks(you know, the stuff you roll opposed to Perception). That's the static +20 in the table for Stealthing characters(d20+20 check). That's the DC20 perception to spot creatures NOT using Stealth. It's not a double dip. You don't get to add up various parts of the table together however you see fit. If you did, a city wall(DC30) with a knotted rope(DC5) next to it might have a Climb DC of 35, not 5. See where I'm going at ?