Keep in mind that modern games generate/compile shader and other caches during runtime, that is one of the reasons for stutter. So when they try version with the drm removed the cache is already generated and so there are no stutters
Shader compilation is well known though, and anyone halfway serious about benchmarking these things (like Digital Foundry) factor this in and control for it
Yes, and anyone halfway serious including DF usually don't find Denuvo having any noticeable effect on performance
DF's claims isn't that it doesn't have any noticeable effect in performance (in fact in a recent video[0] they claim the opposite when Denuvo was introduced to Assassin's Creed Mirage after reviews were done - it can affect performance and thus because of that introducing it after the fact invalidated the CPU performance metrics reviewers had done) but - at least in the cases i remember - they cannot tell if the issues were due to Denuvo or not.
Note though that in a case where they could test both versions, they did find Denuvo to both have lesser performance and affect frame pacing[1] (though that is for a 2yo game, things might be better more recently).
That'd be the case with any update, not just the one that removes Denuvo though.
Keep in mind that FPS drops are only one issue with Denuvo's performance. Another common one (which i think is more common in recent releases, judging from comments i've seen) is frame pracing/stuttering/etc - people very often mention in Reddit threads about Denuvo's removal from a game that the update that removed Denuvo fixed these for them (of course it could also be some other change the game had, but this has been the case with more than one game and games receive other patches before removing Denuvo, so i have a hard time accepting all are coincidences).
A slow/lengthy call every few seconds wont affect your average framerate (which is what often developers check for performance measurement) but it will affect your frame pacing and give a stuttery feel. Most people tend to call this a "performance issue" (regardless if it is due to performance or not).