This worked for me on 11.1 Beta (20C5048k):
Make sure that Rosetta is installed and working, using Safari as a known, working Universal app. Quit Safari
In the Finder, Get Info on /Applications/Safari.app
Select "Open using Rosetta" (you'll want to change this back later)
Launch Safari
If you see "To open Safari you need to install Rosetta. Do you want to install it now?", click Install. (If you do see this message, you likely have had the same problem as me.)
After installation, try opening the Intel app that you couldn't open before.
I encountered this problem on an Apple Silicon DTK Mac mini after updating to a newer version of Big Sur. Before the update, I had been able to run non-Universal apps that had been compiled only for Intel. After the update, I encountered the same permission problems as reported in this thread; I tried several of the solutions below, but they did not help. I noticed that along with the permission messages, I was also seeing "Bad CPU type in executable" in system.log at each attempt to run.
Looks like somewhere among the last couple of OS updates to my current version, 11.1 Beta (20C5048k), Rosetta was un-installed, moved, or somehow de-configured.