In this case Windows moves *.save file to VirtualStore. You will get similar behavior if you remove manifest at all, but I think better solution is to get own subdirectory in user data directory.
Yes, in fact, i never use those *.save .
I created this before UAC exists and I had found easier to put this file in the app directory. With UAC, its different and I don't like virtualisation so i think, like you, that the best solution is to put this file in the user data directory.

Then, i don't know what is the better solution: no manifest or manifest with RUNASINVOKER...

And thank you for your remark about the registry: I have made before several tests with manifests and the results were incomprehensible: in fact, on my machine, this registry key was on RUNASADMIN and , even after modifying the manifest to RUNASINVOKER and reinstalling TYPViewer this key remains the same!! I delete the key, install TYPViewer (with manifest set as RUNASINVOKER) and now the key as the correct value, corresponding to the manifest...