I don't know what you think compacting is. But it is not what you are describing.

Compaction is the removal of dead and discarded data from the MBOX file Thunderbird uses to store mail, It is a housekeeping process where mail that is marked as deleted from the folder is not included in the data when the file contents is copied to a new file and the old one is deleted.

Occasionally there have been bugs in the compacting process, most recently in the 128 initial release See https://bugzilla.mozilla.org/show_bug.cgi?id=1903174. Compacting has never occurred on a timed basis at all but the rewrite that made it to V128 is discussed here https://bugzilla.mozilla.org/show_bug.cgi?id=1890448. I am not aware of any setting that might cause it is fire based on time. The automatic process is fired based on the amount of space in a folder that is occupied by the mail in the folder marked as deleted. The mail is actually removed instead of simply being hidden.

See https://support.mozilla.org/en-US/kb/compacting-folders and https://support.mozilla.org/en-US/kb/compacting-folders-potential-complications

So in other words, what you're saying is that all of my mail older than 30 days old is being deleted completely and no longer accessible or recoverable at all. Also, it only affects my inbox and not my trash mail or my spam either. Usually it's not exactly 30 days, so maybe it's approximate. (Maybe I just hit the storage limit every ~30 days.) I actually have compacting turned off, but it still happens. Also, for reference, I uploaded my disk & index settings.

That little image asks more questions for me than it answers.

Why would you be allocating 140GB of your local hard disk to a temporary cache. About the only reason I can think of manually setting cache would be to limit the space used on a small disk. If you have 140Gn doing nothing clearly that is not the case so why try and over ride the automatic process?

Your coworkers clearly know more than I do perhaps they can give you the bug number for this rather bad bug I need to be aware of something like this. Or perhaps they really do not know so pull out the "bug" response. I see it here all the time. Anything that works by design in a manner other than that which the unread assume it will is a bug.

I would be more inclined to think your mail is on an IMAP server and it automatically takes action to delete or archive mail in the inbox on a timed basis after it is received/downloaded/ read. Folks think that they can click a few setting on a local app and force the server to do things their way. The exact opposite is true. An IMAP server is the canonical source of information about what mail is in what folders in a mail account. Nothing you do in Thunderbird or any other mail application will override setting on the server unless the server admin allows it.

Is you mail on a corporate server? What is the mail retention policies of your organisation? Have you asked the mail administrator?

If you mail is held on one of the large public providers you might mention which it is. I am aware of a number of peculiarities with the various big providers, but it is smaller corporate mail policies which appear to trip folks up. They tend to think email in Outlook is the same as gmail is the same as Yahoo is the same as the company they work for. It is a bit like a motor car in reality. They all share certain features, but no two brands are the same.

I really have no idea what is happening because I really have insufficient information about your setup to make specific claims. What I do know is I really doubt compacting is happening, or has anything substantive to do with your issues.

My guess would be a message retention setting on an account or folder is being fired. IIRC for Thunderbird that happens every 5 minutes.