I can believe he may have put funds in and may have done so legitimately, but the fact is that even if he used his own money towards it, any salary and profit offsets the amount he has funded, even if partially. It's like buying a TV for £150 and then getting someone to give you £50 back to ease your outlay. Either way it's still wrong and it also doesn't impact the contract he has with his "donors".The more there's talk of Alec funnelling money into the production, the fishier it sounds. Disregarding the ever-changing amount it increasingly sounds like he looks at money brought in by either Axanar donations, studio rentals (if there's been any), Propworx auctions or any of his other interests (let's assume he has them to allow for the amounts he's saying he donated) as just one big pile of money that's getting moved around.
I'm no accountant but saying that profit from the Propworx auctions was donated back to Axanar sounds odd. If you hold an auction, and end up 30k in the black from it, isn't that Propworx money? Can Propworx just dump that into Axanar? If you take Alec at his word there are not inconsiderable sums of money being moved around and I have to assume that's going to have implications.
There's also the possibility that he didn't start putting money in it until the law suit in an effort to keep it afloat (I'm speculating) and the salaries may predate his financial input.