I think the general consensus across programs is not to check-in mobile unless you will be arriving late and want to make sure they don't give your room away.

While it may not affect your upgrade odds at some properties, others may not touch your room assignment once you've checked in, which could deprive you of an otherwise available upgrade.

Another exception is if they've already upgraded you, you might want to check-in in an attempt to lock-in the upgrade. I've done this with Hilton when they've pre-upgraded me to a suite. (Although Hilton is a little different b/c their app actually shows you a room map and allows you to pick a specific room.)