What Alt= is supposed to do

The process sequence of creating a glossary entry is different from Shorthand.
It is based on the assumption that you think of or encounter a word or a phrase that you don't want to type out in full once more. So if it has already been typed, you highlight it and press the hotkey Alt= to enter it into the Add Glossary Entry window. In most client applications when linked to Instant Text this hotkey opens the Add Glossary Entry window and pastes the highlighted word or phrase into this window provided the Clipboard works.
Instant Text assigns at the same time a short form which you can, of course, overwrite to your liking using Shift Home to highlight the shortcut.
As you have found out, the snippets and the snippet glossary have nothing to do with this process.
Alt= always adds what is on your clipboard. If it does not enter what you highlighted, but a previous clipboard entry instead, there should be a reason.
My question is can you reproduce the issue you are having at will, or does it work sometimes, but not all the time? The best would be to contact tech support.