There are two relevant points I'd like to make on .aliases files:
1. Alias files should be excluded from your VI package. Do not include them. LabVIEW will automatically generate an alias file when your project is opened into memory. This includes when a copy of your source is scripted, creating a <Your App Name>.aliases in the source code folder.
2. The .aliases file create in the source code folder will not be removed by VIPM during uninstallation. This is expected behavior, as the file was not installed in the first place. Don't worry about uninstalling this file - leaving the file behind is acceptable at this time. Feel free to use a post-uninstall VI to remove any leftover files if you wish, but we will not be worrying about these minor files being left behind at this time.
Hopefully this is helpful to some of you. Thanks everyone!