I think you over-state the position of strength McInnes was in at the time of negotiating his extension.
Whilst the Bosman ruling was just around the corner, no-one knew what the judgment was going to be. Also, the Bosman case (and judgment) related to transfers between EU member states: it did not in itself relate or apply to transfers within the same member-state (this was a later adoption).
He was also not "in demand" at the time of signing his extension: he was in dispute over offered contract for some time before eventually signing and was not linked to any clubs during that summer period. He could have signed elsewhere if another club wanted him and was prepared to either meet our expectations or go to tribunal, but he didn't seem to have any attractive offers. He was our star player, but was still relatively low-profile at that time.
That aside, confidentiality clauses are common-place in employment contracts; mine has one and I suspect most football contracts are a standard form which includes such a clause. In the vast majority of cases there is no reason to object to a confidentiality clause, but insisting on its removal would send red flags.
I doubt the escape clause had it's own confidentiality clause, but suspect it was captured by a general confidentiality clause covering the entire contract. Wilson was quite explicit in the media about the contract having a confidentiality clause and McInnes/McMurdo breaking it. Had there been no such clause, the obvious response of McInnes/McMurdo would have been to admit to leaking the escape clause because they were perfectly entitled to do so. But they never admitted it, and they also never sought to argue that there was no confidentiality clause.
More likely that McInnes/McMurdo accepted the clause because: a) any bid from a genuinely interested Premiership Club would have exceeded the 250K threshold anyway, b.) if need by they could always leak the threshold figure with effective impunity, and c) in the event of Bosman going the way they hoped, McInnes would be able to escape at the end of his new contract regardless. All three of these factors came good.