How to delete all iOS Mobile Applications in iTunes except ones being used?
Apparently (based on a comment on my answer in the question you linked), syncing a device with iTunes no longer transfers purchased apps from the device to the computer.

There is no automatic way to "restore" all apps that you want into your iTunes library. Each one would need to be re-downloaded through iTunes. From the Apps section of iTunes, if you go to the App Store tab, there is a Purchased link on the right-hand side a few items down. From there just click on the cloud with the down arrow in the corner of the icon for each app you want to re-download. you can sort that list alphabetically using the Sort drop-down toward the upper-right.

I don't know if there's an easy way to get a complete, alphabetical list of all 3rd-party applications installed on your device. Settings > Cellular will show you a list, but I don't know if it's complete. (I think it should be, though.) Settings > scrolling down past Apple settings will show you a list, but I believe it's only apps that have permission requests built-in, or something exposed for the settings app; I don't believe it's everything. Settings > General > Storage &amp; iCloud Usage > Storage > Manage Storage will definitely show you a complete list, but it's not alphabetized. 

You are correct that, even when apps were copied from the device to the computer, user data was not included as part of that. Data from apps is only copied when making a backup.