It is tempting to say it /never/ ends cleanly, but honestly it is more like 9 times out of 10.
My environment: Windows-XP in a public library. PAC on a USB stick. Thunderbird P.E. 45.1.1. Network painfully slow.
When I get a 10-minute warning that my time is running out, I shutdown all my apps. Thunderbird appears to go away.
Then, after waiting a few minutes, I try to exit the PA Platform. It cogitates for quite a while. then tells me that T-bird is still running.
Usually, I tell it to try again. Eventually the Mozilla Crash Reporter informs me that Thunderbird has crashed.
When I dismiss that, I can safely exit PA and reclaim my stick. Usually.