Here's your answer: The GM's wrong. The rogue archetype poisoner's extraordinary ability master poisoner does exactly what it says, and the rogue doesn't need to change the poison's delivery method during the poison's creation nor create the poison himself. The special ability says that the rogue "can use Craft (alchemy) to change the type of a poison. This requires 1 hour of work with an alchemist’s lab and a Craft (alchemy) skill check with a DC equal to the poison’s DC. If successful, the poison’s type changes…. If the check fails, the poison is ruined." That's a poison not any poison the rogue creates. And doing so requires 1 hour of work in an alchemist's lab; it does not requires 1 extra hour of work in an alchemist's lab when the poison's created. Done. Really, that's, like, inarguable.
But your GM is arguing with it anyway. So while that's the answer, I suspect that this isn't actually the solution to this problem. I suspect one of the following lines of thinking is making the GM look askance at this ability:
The GM thinks the rogue's A. muscaria poison will unbalance the campaign if its delivery method's changed
This problem is the most easily solved: simply ask the GM to revisit the effects of the A. muscaria poison. Explain that the effects are probably, by Pathfinder standards, too extreme. (The only reference for an A. muscaria poison I could find is this 2017 Paizo messageboard post in the Thrushmoor Terror spoiler; it's unofficial although adapted from material by a Pathfinder designer and uses the Diseases and Poisons Optional Rules, which I suspect you're not using, so I don't know what effects this poison has in your game.)
If this is the problem, the GM could totally be correct: It's possible the effects are too extreme. Further, the GM might've allowed the rogue to create the poison without realizing the rogue would later modify the poison. Thus, in an effort to save face (and the campaign), the GM's arguing with the special ability.
That is, sometimes a GM believes he's made a good call, but when the call's effects reach their conclusion, it seems too late to reverse that call. So, rather than reversing the call, the GM argues against the call's anticipated result. I've done this—without realizing it—as a GM. I mean, I try not to,— and no one does this deliberately—, but at the table in the heat of the moment and absent reflection, it totally happens. But it's never too late to reverse a bad call.
So if the GM did make a bad call about the effects of the A. muscaria poison, renegotiate the poison's effects then explain how you'd really like your rogue to use the extraordinary ability master poisoner as written. Even say please because being a GM is hard. However, I strongly suspect that there's more to it than this—y'know, since the GM sort of, a little bit, called you a liar—and that an overpowered homebrewed mushroom poison isn't really the problem.
The GM thinks the campaign's rules make the extraordinary ability master poisoner too powerful
Crafting a poison requires spending gp for raw materials and requires a great deal of time. If the GM's waived the raw materials gp cost if the rogue gathers the raw materials and the GM's reduced the time to create the poison because the A. muscaria poison doesn't have a listed price or because it's just boiling mushrooms or whatever, then, in the right campaign, the extraordinary ability master poisoner needs the brakes put on it because the rogue's going to poison the crap out of everybody all the time. The only defense NPCs will really have is immunity to poison (which, short term, is easily achieved), but then your PC can't do what he does best. That's no fun for anyone. The GM has to prepare for your PC to poison all the NPCs, and you have to be ready to play Smash Bros. because your PC's best abilities are all nerfed.
If this is the problem, consider revisiting the rules. They're there to make creating poisons expensive and time-consuming. Without those checks, the GM must intervene if he's to continue running the campaign he imagines instead of, for example, a campaign that sees PCs defeat their foes by hurling at them sponges soaked in hallucinogens.
The GM thinks the campaign world makes the extraordinary ability master poisoner too powerful
It's possible the extraordinary ability master poisoner is too powerful and needs some restraint if the campaign is such that the majority of foes are not immune to poison and temporary immunity to poison is not readily available via the 2nd-level spell delay poison (which, if you haven't already read it, you should now—the spell totally upsets the poison applecart by the time PCs are facing foes of level 3 and higher). In a realistic, largely nonmagical campaign wherein the foes are mainly humans—Renaissance Italy, I'm looking at you—, the ability to create contact poisons from ingested poisons is awesome and nearly magical. If this is the case, you're kind of sunk. No GM wants the king of Naples slain by a series of Wolfsbane high fives.
This might not be the solution hoped for, but if this is the case, negotiate with the GM to make the conditions needed for modifying poisons using the extraordinary ability master poisoner more difficult. Maybe modifying a poison takes an expansive alchemy lab only available for rent in a large city at an exorbitant price. Maybe modifying a poison takes not one hour but one week. Maybe modifying the poison costs the poison's cost again in reagents. The GM's permitting an overpowered special ability into the campaign, and that's risky for the GM, and the GM deserves some respect for that, but the GM needs to talk to you about it, too.
In conclusion…
It's possible I'm totally off-base, the GM misread or overread the special ability master poisoner, and all it takes is a few answers on an RPG Q & A site to make the GM recognize his error. But if you think the issue may be bigger than that, it might be worth considering the alternatives above. Or—as a last resort—playing a different character.
