Launching .NET Core executable when Custom URL is opened
So as it would turn out, Apple doesn't like you having multiple copies of an app as backups.

Usually when I'm doing this kind of executable/package work, I keep backups, such as BAK1_Package.exe, BAK2_Package.exe, etc.

It seems that if you have more than one .app that's registered to a URL handler anywhere on your system then Mac uses one of those, and not specifically the one that's in the Applications folder. So when I tried to launch the URL, instead of launching the most recent .app that was placed inside the Applications folder, it was launching the first one that was in the _BACKUP folder on my desktop.

For anyone else who runs into a similar issue like this: make sure you only have one .app registered to that URL handler.