It's good to be precise with terminology and facts, especially in legal matters.
I'm not privy to the specific words that were exchanged, so it's hard to be precise. But I imagine it was some form of Trump saying "by tomorrow, I will give you a 90-day extension. I have a gentleman's agreement with the current government that if you do not stop your services in the 24 hours between now and my inauguration, you won't face any issues, so please carry on and we will clean this mess up later".
If you want a private citizen analogy, it's similar to someone saying they won't press charges despite a third-party being in flagrant illegal behavior. In this case, it's the US government saying they won't press charges. Both Biden and Trump have said as much, if my understanding of the case is correct, and one can assume they have discussed this with the appropriate branches of government.
If someone challenges his interpretation of the 3 requirements in court, then presumably he'd have to explain why he believed that to be the case[1], but he does not have to prove this certainty ex ante in order for the 90-day extension to be valid.
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[1]: IANAL but whether he can successfully prove it or not is also ultimately irrelevant given the SCOTUS recent interpretation of presidential power. If he's found "guilty" of making a bad interpretation of the certainty of the 3 requirements, what is really going to be his punishment? There's really nothing you can do against a sitting president with regards to the exercise of their executive power...
“there are in place the relevant binding legal agreements to enable execution of such qualified divestiture during the period of such extension."
This is a binary thing. No such legal agreement seems to exist. You also ignored the other parts of my comment about him missing the deadline in the law to apply the extension.
Johnson himself said they will enforce the law. https://www.nbcnews.com/politics/congress/speaker-johnson-2-...
The definition of certify is literally "attest or confirm in a formal statement"
Besides, there's no process through which Congress would question or investigate whether the president really can or cannot certify whatever he claims about this matter.