I need to be able to have certain keyboard shortcuts disabled when I'm using Microsoft Remote Desktop, but enabled everywhere else. Is that possible?
There are multiple ways to achieve this.
The easiest if it's only a few shortcuts, define them separately for the Microsoft Remote Desktop app, and disable them (cmd+d or right-click => disable). Instead of disabling you can also assign the "Use Apple Default Or Do Nothing" action.
Alternatively you can create a conditional activation group that matches everything but Remote Desktop
Thank you, this looks like it will work.