It appears that after restarting TB due to an extension change or whatnot, the launcher thinks TB is done and closes. While I haven't lost any data due to this (thankfully), seeing as the launcher usually doesn't clean up until Thunderbird closes, I doubt very much that this (launcher closing on restart) is the desired behavior.
Note that Notepad++ also has this issue (where it does cause issues), and I'm guessing FF does as well.
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Restarted are allowed for in the Firefox and Thunderbird launchers and work fine in my testing (you can see the code handling it in the launcher as well). Notepad++ appears not to due to its new extension system (which is not currently supported).
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Is the launcher supposed to quit after a restart though? It normally stays around while TB is running, so I figured it should keep running after a restart as well. Like I said, I haven't experienced any adverse effects from it myself (I only discovered the quirk by accident because I had Task Manager open at the time), but the behavior struck me as a little odd, is all.
It sticks around and did the last time I checked. Basically it runs TBP with an ExecWait so that stays until a restart. Once closed, the launcher will wait 2 secs and check to see if TB.exe is running. If it is, it checks for a parent.lock in the profile directory (which TB does to indicate a profile is in use) and when it finds it, it continues to wait for the process to exit.
So, in short, TBP.exe should stick around to wait for TB.exe after a restart the same way FFP.exe does for FF.exe since FF 3.0 (which introduced this behavior with extensions). The only time it will not is if you're running multiple instances enabled in which case it may not work properly.
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Just tested it now by installing AdBlock Plus and ThunderbirdPortable.exe disappeared from Task Manager in the middle of the restart process. thunderbird.exe never disappeared from the list though, which leads me to believe it restarted quickly, but must not have created the parent.lock file fast enough.
I'm using TBP 3.0 if that makes any difference. And this is on my netbook, so perhaps 2 seconds isn't enough time...?
Edit: Tested again, this time installing ThunderBrowse, and TBP.exe stuck around. I'm thinking my hunch is right--TB sometimes isn't creating the parent.lock file in time, so the launcher cleans up. Is there any way to test for a specific executable, i.e. with a full path, rather than just by filename? That'd avoid the need to test for parent.lock, I think.