Only the Doom FatBoy hovers. This was to make it a greater threat to Naval players. The small Gap at position 13 can only be reached by hover units, as the underwater terrain is too steep for units that walk.
Though, mute point, I did move Position 13 back (you said some players really like that position) to the peninsula that is further north, and added a small wall (half the height of the current walls) to make the position a little more forgiving. Or should I keep 13 where it currently is? I did shrink the walls there as well.
Beach defense is always going to be difficult. I've tried to make it easier by switching the old artillery positions (the ones for the scripted coop) to work for defending the island. I moved 1 spawn from NW to the beach, so there are now 3 spawn positions for beach defense. They are grouped together on the West side of the beach, so they may provide support to each other. East side of beach/peninsula has no spawns, but is an optional expansion area for beach players. Difficult to hold if navy doesn't do their job well.
I did watch your replay and saw the traffic jam. Looks like it saved you. T4s were pathing through it, trying to go different ways and holding each other up. Can fix by opening up the area a little more.
The teleporting doom is not a feature. Seems that was a bug. Don't know if it was related to the game not properly ending. There are flags that should stop all scripts from running once HQ is detected as destroyed.