TL;DR
Concrete usage of mods as the intended way to play, by allowing players to manually toggle exact mods to not interfere with global steam achievements.Why ?
I played with QoL mods since my first factory, and because of that I missed a lot of achievements; so last few weeks I spend completing them all... And since I always played with mods, playing without wasn't a great experience for me — I felt restricted in a way that isn't interesting, doesn't add any value to achieving achievement, and simply inconvenient; which made me think about why you, devs don't allow to use mods and how it can, and why it should be changed...It shouldn't break anything or be a vulnerability that allows players to "cheat"... since it's already pretty easy. I got my first rocket achievements on Steam, even though I was using mods, including creative, which I used to actually "cheat" and decrease evolution on my first world; and all I did is just reloaded save without mods. Without mods you can do that only with cheat-commands, which are considered as cheat, and which use is disabling achievements for this save...
For the people who play mods that extend Factorio beyond vanilla limit, and which may not want their achievements to be accidentally triggered, this should be done so that you can enable/disable achievements with each mod individually, with a warning popup.
It also will establish philosophy that there is no "intended way to play", as some people which denying the use of mods refer to. While beating the game for the achievements I've created a quite few suggestion threads on this forum and reddit, and I don't actually know what was more painful — playing purely vanilla, or getting linked to the mods in almost every of my thread... and even if they literally solve everything, but I can't use them because I'm doing achievements...
(I could reload save without them, but I hate it because my pc is bad and it takes a lot of time)
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So yes... I think this change would be really great for everyone who would do achievement runs. It will make things much better; and, as I argued — I don't see how it can be bad. It also should be the bold point in arguments of the "intended ways to play", and with that there shouldn't be any other reason to decline mods.
(P.S. and again I actually really hated being linked me to mods, loving and wanting them, but being unable to use because of achievements)