CIPA gives the judge the discretion to decide what classified information must be included, what must be excluded, and what information can be left out but with a substitute.
As far as doing this late, it was the prosecution who waited this long to say that they want to just tell the jury about the documents that accuse Trump of wrongfully having, not show them. Who would have anticipated a prosecution strategy of not showing the evidence?
The Judge offered the prosecution an easy way out of showing the evidence: just agree that the jury will be told the obvious truth: The PRA gives each departing president the authority to determine which papers are "presidential," and which are personal. Then, the jury does not have to see the papers. Clinton was able to do that, and the USSC ruled in his favor, so the precedent was set.
If I were Trump's lawyers, I would fight that. I would say "no evidence, no trial. If the jury won't see evidence, how can the trial be fair?"