Networked switches are typically wired somewhat differently the non-network switches so when you replace one switch in a three-way you have to replace them all. It’s not so much that the upstairs Switch would no longer work, it’s that flipping the upstairs Switch might then cause the downstairs switch not to work. The wiring pattern is just different. See the FAQ
And, yes, you’ll be able to turn the master switch on and off from your phone or by voice if you have a device like an Amazon echo. The second switch is just a convenience. If you want to get rid of it you can blank it off, you just can’t leave the old one in place.