I did some searching and discovered that although there's just one desktop, there are multiple viewports. The Ctrl-Alt and mouse switch still work and I can have different apps on different viewports, I just can't click on the number of the viewport like I used to.
There's an option in the Setttings Manager for Viewport Switcher called "Go to specific viewport". There's "Switch to Viewport 1" etc and if you click the edit button on the right, it prefills all of them with "<Control>F1" etc. But I'd just rather click on the app at the bottom unless I want to see the Atlantis plugin fishies
then I use the Ctrl-Alt and mouse.