re :I understand that Thunderbird treats these 5 emails as a thread and marks the entire thread as read. How can I stop Thunderbird marking a thread as read?

If the thread is collapsed and you mark the top level as read then all get marked as read. If you expand the thread and mark one as read then only one is marked as read. This is the standard method and there has been no change to this. It functions the same as previously.

If the thread is collapsed and you mark the top level as read then all get marked as read.

I am not using threads view. I always see all e-mails in the order they were received. I checked and no matter which e-mail I mark as read - all e-mails (5) are always marked as read

Do you have some kind of add-on, such as Conversations, that could be causing this? Help/Restart with add-ons disabled to test.

I had an add-on. I just turned everything off and restarted Thunderbird. Unfortunately, nothing has changed. Still marking one message as read marks all of them

I did a test on an unthreaded folder and marked 3 messages in the same conversation as unread. When I selected one message (making it Read), and pressed R, the other 2 messages were also marked Read. But if I right-click one message, Mark/As Read, only the selected message is marked Read. So, there appears to be a difference between the action of the keyboard shortcut and the (correct action of the) context menu.

I checked it this way, and it works the same on my Thunderbird. Only now how to get around it to work with a keyboard shortcut?

My menu shows the R key to be the shortcut to mark a thread as read. There does not appear to be a shortcut associated with mark an individual message as read.

You're right. I saw it now. So how do you quickly mark individual messages as read? How do I set my own keyboard shortcut?

With tbkeys-lite, I set the m key to mark a message as read (see picture of the add-on's Options).

I noticed that the 'm' keyboard shortcut works without this add-on. Weird. The addon is interesting. Is it possible to set the Ctrl+q shortcut?

So it does, even though I chose m at random. The m shortcut is mentioned here. I think my code is wrong, but it accidentally led to the discovery of the correct key.

I think the add-on documentation mentions that additional keys such as Ctrl are not supported.