It should be noted that several authors/users seem to have changed views from the "norm" of cleaning the master, under the scrutiny of the xEdit cleaning process and issues cropping up with it (I can not cite but have talked to a few privately.) Though, this does seem to be a more recent development with xEdit; cropping up every couple of months this year.
Actually I'm not sure the 'norm' was ever the quite the 'norm' we assumed it was. This is the thread (2017) that prompted me to investigate this issue more closely, specifically DoctorKaizeld's comment: "kinda a well-known thing that you don't clean master files". Note that they are specifically referring to LE, not SE, but that doesn't really matter in this context.
GrantSP (2018) reaches a similar conclusion here after discussion with other mod authors although he admits "there may be some small benefit for Skyrim to do so".
Then there's the anecdotal reports, some linked below:
I think in summary from the AFK Mods discussion...
Trying to look at this unbiasedly, it seems it's really not going to matter in regards to cleaning the master files, but mods should always be cleaned unless otherwise noted by their authors. That's what I got from boiling out the passionately overstated views from the heat-of-the-moment discussion. Oh...and more confirmation that UPs should always be used because they fix things people!
The AFKMods discussion was bemusing to me when I first read it when I was researching this as I read Arthmoor's most recent comment to not clean the masters before I read that thread where he is passionately disagreeing with Mator and recommending they be cleaned.
Anyway, as we now know that cleaning can cause issues and since we appear to not have any cases of issues caused by using uncleaned masters (assuming correct use of patches), I would say that's fairly conclusive.