It's a radio transmitter. If you need to you can put a clear plastic bag over it and seal it to the camera body with gaffer tape. Gaffer tape leaves no residue behind. It's still easy to press the control buttons through the plastic. Or better yet, use a plastic cover made to fit over the flash and the camera. They're cheap and effective. I've never used the YN-E3-RT, but I have used the same method with a Flashpoint (Godox) R2 Pro Mark II transmitter.
The last Yongnuo flash I bought was a YN685. It has a big rubber chunk at the hot foot similar to the one on the YN-E3-RT that is supposed to seal off the connection to the camera's hot shoe. It was constantly falling off to the point I stopped putting it back on most of the time. Most of the time I was using the flash off camera via radio and the flash was mounted on a cold shoe.
Once I switched to the Godox system I needed to attach a Godox X1R-C to the YN685 and did place the rubber chunk on the flash before attaching it to the receiver. But if I'm shooting in any kind of wet weather, there's a plastic bag over my camera, lens, and flash/transmitter.
The whole idea that some things are "weather-sealed" and other things are "not weather-sealed" as if there is no in between is a false assumption. It's not a binary category. There are varying levels of weather/dust resistance. Try immersing the Canon ST-E3-RT in water and see how "weather sealed" it is. Then try getting Canon to replace it under warranty. As Roger Cicala has often said, "You can assume whatever you like, but when you send your lens/camera in for repair, ‘weather sealed’ still means ‘the warranty doesn’t cover water damage’."
