I've been playing Skyrim SE recently and I wanted to see my total modded and unmodded playtime. So I'm trying to see the time played when loading a character. It says I've played 58 hours on the unmodded save and 106 hours on the modded save. So does the 106 hours on the modded save include the 58 on the unmodded save? I personally think it doesn't because it also shows 6 mins as a prisoner at the start of the game separately.
If they're the same character: yes. Otherwise, no.
The same rules still applies for even if you multiverse time travel, save scum, etc.
Unless you have a mod that modifies your playtime stat, just having mods alone will not affect the functions that govern the playtime counter...
As for Steam's counter: That's a seperate thing altogether.