I think this won't be an issue. I say this because of how the Nintendo Switch works at least right now.
Something that is incredible though is sleep mode. When you turn off the Switch, it remembers what you were last doing. So as long as the same game is in the Switch itself, it won't do anything to what you were last doing. If I turn it off in the middle of completing a BOTW shrine, when I turn it on, I'm still in the shrine, and none of my progress has been reverted. If I'm in the Seaside Kingdom in Mario Odyssey and turn off the Switch, I stay where I was with all my progress still there when I eventually come back.
I can only imagine that when you turn off the Switch in the Smash Ultimate fighting menu, your settings won't be changed. I think this won't be an issue so as long as you don't close the Smash Ultimate software while the device is turned on.