I only use the webapp, and the "Use the app messages" was very annoying, until I found that you can actually turn these messages off using some obscure setting (which, of course, I can't find right now...)
It's easy to turn that dialog off 'permanently' (as long as you don't clear the cookies) on any Android browser: When the dialog appears, click on the hamburger menu at the top right of the reddit page, then turn off the "Ask To Open In App" option. The option disappears when it's off, so it's not possible to turn it on manually (not that anyone would want to). I've set it off months ago in my main browser and it's still off.
