It's a reasonable assumption to make that the new ones had adjustments done. Even larger was the unchanged strings. I could easily imagine that the older ones, since they're not allowed to be modified in any way, had older strings than the new ones. That alone could produce a huge difference.
That's a difference, but it's a difference with obvious large implications for using the things in performance as well as experiments. As such, it's hard to see how it's a problem in the experimental design; if you're not allowed to adjust the Stradivarius while it's in your possession, maybe a newer model really is the right choice for a concert?
That is fair; but, my assumption in this situation is that if the musician owned the instrument themselves, they would have been allowed to tune it. Not being allowed to change details may have been a way for the benefactors of the instruments to keep them from being harmed
With Stradivarius violins costing millions and millions of dollars, I always assumed that the people playing on them didn't, in the typical case, actually own them (much like how science is now mostly practiced by professionals funded by grants, instead of by the bored idle rich). But I'm not informed on that point; it could be very different.
I don't know the exact breakdown of numbers, but it's increasingly common for a Strad to be owned by a benefactor and loaned to the musician. I don't know of any other artifact that straddles such extremes of being a treasure but also a work horse. Even the owners of lesser instruments have to deal with the implications of taking a valuable and delicate instrument out of the house to play in a saloon.
For this reason, tweaking a Strad is unlikely to be done casually. Re-stringing? Sure, at the very least E strings, which break all the time. But a set of fiddle strings is damned expensive, and takes time to break in so they don't sound too harsh, so re-stringing has to be coordinated with one's performance schedule.
Online, one can find a list of every known Strad, its history of owners, etc. Interestingly enough, a couple of them are listed as missing or stolen.