The fact that portable programs are added to the all apps section of the start menu.
This, I don't see portable apps in my download folder appear on my All program list. I have few in there too.
The fact that the exclusion on the Downloads folder doesn't work.
I believe, the "Manage custom filtered folders" is not for All program list. It is for the tile area (Groups or tabs)

Thank you,
Basj,
Stardock Community Assistant
End of basj's quote
I had assumed that the portable programs were being added to All Apps automatically by Start11 scanning the hard drive looking for programs. This must not be true. This made me look at it a little closer.
I went to one of the portable programs in All Apps, right clicked it, selected more, and selected Open file location. This took me to C:\ProgramData\Microsoft\Windows\Start Menu\Programs. There I saw shortcuts to all my portable programs. I deleted those shortcuts and the programs disappeared from All Apps.
The only thing I can think of is that before installing Start11, I did pin these programs to the right side of the start menu (the tiles side). That did not add them to the All Apps section of the native Win 11 start menu.
Then I installed Start11 and at this point they appeared in the All Apps section of the Start11 start menu, but not the native Win 11 start menu.
In any case, now I have it the way I want it with the portable program icons added to the right side of the start menu and the programs not added to the All Apps list.
I misunderstood what the "Manage custom filtered folders" list would do. Interestingly, adding the exclusion for the Downloads folder did not remove the tiles from the right side of the start menu either. Maybe a bug?? Or I coded it wrong?? In any case, I don't want them excluded from the right side of the start menu, so I'll delete the exclusion.
Thanks,
Bill