Those Visible Message Actions appear to show or be accessible while reading an individual message. Either a few new icons will appear top right, or from the ... menu top right, there will be additional options.

I raised a sort of bug over this as not all the Options seem to display and some do in places not expected https://thunderbird.topicbox.com/groups/android-beta/T3205c8f2da67fdc9/some-visible-action-buttons-not-appearing

What is the Visible Message Actions configuration for? I checked Spam (Delete was already checked) thinking it might make a Spam icon visible when messages are marked in the message list or when a message is being viewed, but I didn't see anything at all that seemed to have appeared as a result of checking that item. Gear Menu > General Settings > Display > Messages > Visible Message Actions Thunderbird for Android 8.0b1 Samsung Galaxy S21 Ultra 5G/Android 14/One UI 6.1

In Thunderbird Android Ver b4, I was able to check the message with the same behavior after processing it as junk mail.