As a caveat, I'd like to note that too much arguing with your GM is a mug's game. Past a certain point, it's like asking why my wife didn't want me playing Occult classes in her first AP: she didn't want to for reasons of personal comfort. In her case, it was to prevent rules overflow for her first time behind a PF screen; for your GM it could be ny reason. Pushing at that either runs into a Rule Zero loss, or your GM starting a lethal+ type of game like Mythic thinking of your character as the one he didn't want and you as the player who badgered him into a rules change. You don't want that, needless to say.
So I recommend you approach the subject politely, cautiously, and respectfully. And honestly if try three doesn't work, drop it and figure something else out.
That said, your GM is house ruling and misinterpreting punpun-- dramatically, in the latter case.
Textually, calling an effective size increase and a physical size increase the same thing is like saying a racial bonus to will save and a resistance bonus don't stack because they both start with r and don't stack internally. The FAQ clarifies that, basically, no matter the source, all size changes are "size bonuses" and all effectives are "effective size bonuses" and while neither stack with themselves, they do stack with each other. He's layering a rule on top that requires extra reading.
That said, that's his right, so I would not suggest leading with that argument unless he's signalling a willingness to negotiate. Telling you to find a text exception to a rule that isn't in the book is a "go away and don't make me hard no you" social maneuver.
What I would suggest is asking him if he's concerned about punpun actual, or punpun as a shorthand for powerful synergy. Punpun actual is where you get reassuring: the problem with punpun is that there weren't any limitations on how high his strength bonuses were to start, and very quickly, on any attribute, then on getting any ability, period. Like an arbitrary end to a magic the gathering loop, the only controls were when punpun decided to stop buffing and start doing, and time to buff.
If his concern is that, your best opening offer is to say you're sticking with your two sources, period. Possibly even promise you'll stick with a net of +2, no questions asked and everything else goes in different directions. Write a contract if you need to, just make sure that your position that you won't be a jerk if he is willing to work with you, THEN go with "and this is why it works RAW."
If he's using punpun as a shorthand for "powerful synergy" then I'd go with both a written/emailed agreement that you won't keep pushing this, and point out you're still playing a martial character with few tricks for flexibility; there's really only so far you can go prior to the point when other direct damage types are one hit killing, anyway.
But, like I said to start, take a hard look at whether or not you want to pay the price of putting a target on your PC's back, potentially even after losing anyway. He's functionally said no twice. It may be a better idea to look for a different way to add oomph.
