Have you ever actually heard anyone mention the application of anti-fungals to citrus fruit rinds in the first place? Because I've never even heard of it outside of mycology circles, and there are virtually no Google results despite the fact that the practice is ubiquitous.
How does "There is virtually no evidence that this is even done" translate to "This is a big problem"? At least in my book, lack of evidence doesn't count as evidence.
Actually a Google Scholar search for 'citrus postharvest antifungal treatments' does show that this is in fact the standard operating procedure. E.g. this paper starts out with a summary of the current state of conventional agriculture:
"There is utterly no epidemiological evidence that eating zest has anything to do with any kind of fungal infection."
No, but there is plenty of evidence that fungi develop resistance to anti-fungal drugs. If I really liked zest I might keep eating it, but since I actually don't like it in the first place I don't find that I lose anything by leaving it out of recipes and cocktails.
I certainly wouldn't say that it's definitely harmful, but when you're eating all these fungicides that have never been tested for longterm safety on humans then that's a risk one should be at least cognizant of.
Actually unlike antibiotics, there is limited evidence of rrsidtence to antifungals. Amphotericin and fluconazole have been around forever and still useful.