Currently there's a task running on my system with an estimated time remaining of 5 days 7 hours, but the deadline is already in 3 days 21 hours.
(Hardware resources are heavily throttled in my configuration. I would still like to contribute however.)

I am wondering how Boinc handles these cases and I would suggest that tasks are put on halt when the estimated time remaining exceeds the deadline.

The estimation could be updated whenever settings are changed. If the estimated time is inside the deadline again the task could be continued.

Additionally, in my configuration tasks are switched every 30 minutes which could contribute to an inaccurate estimated time remaining.

(If this question has been asked before I would like to apologize in advance. Boinc version is 7.14.2.)

Frequent task swapping will not help your situation.
But if have just started a particular project the initial estimates can be wildly pesimistic, often by a factor of ten or more. Much the same applies if you have just done a major hardware upgrade. In both cases it can take about a dozen 'normal' task commpleted and validate to get a more realistic estimate, even then you can expect it to take good few more for things to settle down properly.

And while it may not be relevant to you, running windows BOINC in WINE results in the computers speed being under reported to BOINC with the result that estimates in WINE where I have compared with Linux are between three to five times as long given similar histories with the task types.