(Click to enlarge)

(Click to enlarge)

Ok, what this boils down to is the addon export tool is originally designed for addons with no registry hook, and addon.inf was supreme. Actually there were no such thing as a registry hook when the addon management was originally implemented.
Since then, registry hooks are used to identify how addons within the git repository and bundled addons are composed. They are not needed, but it's a tidy way to do things.

I have made some changes...

1) If you select a registry hook when choosing files for your addon, it will pre-populate the fields that go into addon.inf, and you will be advised to not change them. (I don't want us to be dynamically rewriting the registry hooks).
2) If you select *only* the registry hook, it will automatically select all other files referenced in that hook.
3) If you select a registry hook but a different set of files to what is mentioned in the hook, it will exit with an error message.

This way, you can essentially defer to what the registry hook is saying when exporting addons.

I have tested uninstall an addon and didn't find any issues, other than the filenames were poorly sorted. I can see inconsistency in filenames between your 2 screenshots, so that probably explains it - you were probably debugging, or inconsistent with how you defined your addon files (the first part of this problem). Once an addon is installed, the registry hook does take precedence, so there's definitely scope for inconsistency prior to me resolving this issue.

I noticed the different filename on the image shortly after, sorry, but I think it was left behind (or removed and marked as will be overwritten upon reinstallation) before I renamed the file also. Thanks for the changes though, brilliant.