Pretty sure he's referring to the Brooks article in which he states sources informed him that the NYR agreed to pay the bonus only if the 2nd was included.
Now, whether you choose to consider anything from a Brooks article as fact is up to you, he's got a questionable reputation, but doesn't tend to historically outright make up stuff like this.
That said, the timing still seems odd, as if there was a deal in place that was just pending the payment of the bonus, it probably would have been finalized right after payment, which I think was 1 Jul, instead of almost 3 weeks later.
There is certainly value to having had NYR pay the signing bonus, and it would be naïve to think there wouldn't be some sort of asset moved to offset that. It possible that we always intended to 'buy' 2 mil with a 2nd rd pick, or it could be that that cost was negotiated after the bonus was paid because they just hadn't come to terms on the trade prior to it being paid. Brooks certainly implied that it was negotiated in advance, but we're dealing with 2nd hand (at best) information here. We don't know how close Brooks' source was to the negotiation, so there's a good chance of some conjecture going on here.