Does playing with a different user active on the Switch create a different file?

As with almost every game on the switch, your save data is tied to your user account. Each user profile on the Switch has their own save data.

However in addition to this, with the new Switch Online program, Smash Ultimate supports Cloud Saves which will backup your data on the Nintendo account your switch account is linked with. This means that you’ll be able to pull save data down from the cloud onto another switch if you so desired.

So your save data is both linked to the local User Profile on the Switch and (if you use Cloud Saves) to the Nintendo account the User Profile is linked with.

I just tried this and all save data for this game appears to be tied to the account you play with.

I started up with a second account and everything was running as if the game had been started for the first time. I re-unlocked an Eevee spirit for Let's Go Eevee save, the fighter roster was back to the initial fighters, the World of Light had 3 open save slots, Challenge mode and all other stats had no values.