Would it be proper grammar to use the Latin phrase in the following way?
The items inserted came from departments, employees et al. data.
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No, that's improper (and confusing).
The normal use of et al. is for a listing of names (as in "the paper was written by Fredricksen, Mayer, Wilson, et al."); for a listing of generic objects, et cetera (or etc.) is the standard choice.
Moreover, using either et al. or etc. mid-sentence is very disorienting, as it is normally reserved for a terminal position only. Most often it's used at the very end of a sentence because the list it's being applied to is also at the end of the sentence, but it needs at least to be at the end of the list. Your list is "departments data, employees data, other data"; the call for a parallel structure ("department, employee, and other data") is clear, but et al. and etc. replace "and others" (where others is a pronoun), not "and other" (where other is an adjective).
So, either don't use etc. or reduce the parallelism a bit: