And cover the flask with some shrink wrap (maybe with a tiny hole punched into it) to hinder steam release.

I actually miss the stretchy shrink wrap, it was pretty useful in daily lab life

Parafilm? 100% agreed. I’ve thought about buying a roll, which will probably last me for a lifetime. One of these days, maybe.

Yeah, that is always an option. However once boiling hot, if you introduce something into the flask it's more likely to create an explosion front. A bit like when someone supercools a bottle of water and then taps it to make it freeze; except with exploding sticky gel, and it's as hot as lava*

*Not actually as hot as lava, but wow does it feel like it

I wouldn't worry about that. I've poured hundreds of gels and added the EtBr to it after microwaving it every single time. Never had anything close to that happen. Just use a sufficiently concentrated EtBr stock and you're adding like 45 µL to 45 mL.