Two question for you...
1. I got to look at her perforation and the doc said as well that the edges of it were thickened and scarred over. It did not look like a new perforation, and it made no signs of closing on its own after 3 months. We were wondering if it's likely the perforation had been there for some time and she was diving with it unnoticed. Do you think that is likely? We dive 100+ days a year and we're in the water several weekends each month of 2023 before the perforation was discovered in December/January after her infection.
Hard to say much about ear stuff over the Internet, but it's pretty unlikely that you would be scuba diving with a tympanic membrane perforation and not have any idea that it was there! Maybe a very tight fitting hood kept it dry?
2. I realize this is not recommended, but in theory if she had an earplug or silicon ear cover that fully sealed her ear off, that wouldn't cause any problems since there's no need to equalize that side, right? She just needs to keep all water out of her middle ear, or am I misunderstanding the risks?
No one is going to "clear" you to do that. There are risks of ear infection if water gets in, risks of sudden vertigo underwater, risks of chronic damage... and the only way that you wouldn't need to equalize would be if the middle ear flooded with water, right? It's hard to get a reliable seal with a plug, and then you would have to rely on ventilating the ear canal through the perforation. Just not a great idea.