As noted above the factory mounting position is on the back left of the battery box. The original flasher came with a rectangular piece of rubber with to slots on it that hooks between the flasher and the battery box. Mine was always mounted plug upwards and never ran into any issue with water logging that I noticed.
Since I switched to LEDs for flashers, I got the electronic flasher which unfortunately doesn't have the tab on it that the factory flasher did to mount in the factory position. I ended up zip tying it sideways to the rearward piece of wiring harness running left to right across the frame.
seems to be working great so far in all the monsoon like weather I've been getting caught out in.
......I'd rather wake up in the middle of nowhere then in any city on earth.
*2014 VN900 Custom (16,200 miles and counting)