It seems odd to me that she would force them to get clearances before settling the matters of law: does the Espionage Act apply to the documents in question,

This boils down to do the documents contain national defense information?

The charge is "willfully retaining national defense information." The indictment rests on the basis that these documents are currently actively classified. (Classification is not used in the Espionage Act because this law was writing before the modern classification system, which is WWII era, was set up.)

But basically if you prove classification, you prove national defense information, so they are connected. The government would have had to provide testimony to the grand jury about this.

Was the evidence obtained appropriately (IIRC they flipped one of Trump's attorneys to turn over written notes from client discussions).

This already went before a judge. They didn't flip the attorney. The judge agreed with the DOJ that in this case the lawyer should be compelled to testify about his audio notes. This relates to the obstruction charges. He is still Trump's lawyer on another case. So this lawyer will have to testify at trial.