Even because OP is a paying customer. We can find workarounds, but only they can resolve the issue.

It doesn’t matter where you installed it from, it will behave as a store app for some reason. What if you disable all app updates:

This won’t affect windows security updates, only updates for apps like notepad. You can still update them manually ocasionally.

Other hacky option I’m thinking of: the store reads the version number of the app from somewhere, I guess somewhere from the registry. Try to find the registry value and change that number to something very big. Then the store will think your version is newer and it won’t try to overwrite it. Be careful with the registry.

Where do you see this dialog? Is it in the settings app? In the settings where? Can you share a full, bigger screenshot? What are the options in the … button in the end?

Never seen a program which updates like this, that’s why a bit more context would help.