I think it depends. FireTray has a lot of settings that users can configure as to how it behaves. Go (menu) Tools > Add-on Options > FireTray and you'll see how it can be configured.
To be honest I only came across FireTray a few weeks ago and was using it successfully in Thunderbird 52.9.1 and I really liked it. Then I upgraded to Thunderbird 60.0 and I couldn't get FireTray installed first time round. So I was only using it for a few weeks in the old Thunderbird then I switched to Thunderbird 60.0 and managed to work out how to get RBTray to minimise the new Thunderbird to the System Tray. (RBTray couldn't minimise pre-60.0 versions of Thunderbird but I knew that Firefox Quantum had changed the way the minimise button on Firefox was coded, so I guessed that change might have been passed-on to Thunderbird 60.0. My guess was right, and after a little bit of experimentation I understood how to minimise Thunderbird 60.0 using RBTray.) So, in all, I'm not the best person to comment on how FireTray can behave with its multiplicity of settings. As best as I can remember it can hide things and show things according the user's own preferences.