Here in EASA land, it's the Part 21 DOA, TC/STC holder (which are Part 21 in EU; US, Can and Bra orgs accepted under bi-lateral) that make the determination often with further approval from the Competent Authority or EASA. Flight outside the MEL? Should that happen?
Fact remains that you cannot generally deviate from approved data. (Having said that, Part 145 does have provision for that under certain circumstances but not those we are discussing here).
You cannot unilaterally alter the aircraft's configuration; the whole basis of approved maintenance is to keep the aircraft at its TC/STC status. I know of an operator that has had its hand smacked for taking units out of aircraft for maintenance and flying with holes in panels and other tricks of that sort.