Gen 3 maintains two save blocks; one for the most recent save, and another for the save prior to that (which acts as a backup). The only time you will lose all your progress and be forced to restart the game is if both saves give a non-matching checksum, i.e. both saves are corrupt.
There is no such thing as a meat shield or a special structure for an "attempt to load the game". There is just a primary save file and a backup save file for when the primary save fails. If both of those fail, then you have to restart. If only the recent save fails, then the game can use the backup.
The game doesn't hold onto corrupt save files; it just writes over them the next time you save. So there is no such thing as spending chances, because corrupt data does not persistently occupy either of the two save blocks.
So, to respond to each question:
Is my FireRed save file becoming corrupted only to work again something to be concerned over?
Not in your case, as the problem seems restricted to XD writing save data incorrectly.
Does this mean that if the trade error were to happen again that all my progress would be gone for good since I’ve already used up the “attempt to load the game” file which is essentially a meat shield?
No
Should I just start over on FireRed so that I can get my two chances back?
No
Or do the two files infinitely replace each other, making this whole “only two chances” thing nothing more than me coming to the wrong conclusion?
Yes to all.