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Perhaps someone with a deeper understanding of how email programs function can provide some insight. However all the mail that is in the Thunderbird Inbox is decrypted. I'm not sure I follow their logic but I can see where you might be defeating the purpose of having encrypted mail if you are going to scatter the incoming mail to the winds. Even though you can create sub folders and filters on the ProtonMail platform you are not allowed to do the same within your Thunderbird account for the ProtonMail for some reason.
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The only problem I have run into is ProtonMail puts all incoming mail into the Inbox on their server by default. I very recently became a paid ProtonMail user and I have found the interface between ProtonMail and Thunderbird works very well.
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