This assumes the mites are what kills the bees. What is that asssumption is flawed?

No. The mites are not what is killing the bees.

And, by the way - natural pathogens exist in just about any population. These very, very rarely led to extinction. There is a media trend to claim the mites are at fault. This reminds me of prior fault yielding e. g. "mad cow disease" - and then the media also stopped doing any further investigation at that point. It's as if they have break points where you can not go past those points. Now it is the mites that get blamed.

To add, varroa quickly gains immunity to the pharmaceutical treatment we have, so the same medication cannot be used 2 years in a row. Most popular treatment from late 90s that used to kill 99% of varroa is now completely ineffective.

It was explained to me this is well planned and solved in Czechia. Varroa treatment is refunded my the government, but only one type of medication every 6 months. It's cheaper for beekeepers to use whatever the government gives them for free, than use something else. And the medication is free only for a few weeks, so everyone will use it at the same time.

Probably, but not at any meaningful concentration.

As article suggest - it is fully biodegradable. I suppose venom has some short half-life. And since peptide is isolated, not full chain toxin, it should be harmless to humans.