I believe this also happens on land when a vehicle is placed somewhere, for example "vehicle setVehiclePosition [[XYZ], [], 0, "NONE"]; (XYZ with Z: height ATL =0)

This sounds very similar. Not sure, it happens rarely and for my means to analyze, randomly. I described in the link below, in case helpful.
https://forums.bohemia.net/forums/topic/239334-wheeled-vehicle-engine-wont-turn-on-not-drivable/

The only solution I have is to replace by a scripted function checking vehicles every few secs:
"vehicle engineon true; -> sleep 0.1; If (not isengineon vehicle) then {moveout crew, delete vehicle, create new with same crew and stored vars}"

The only solution I have is to replace by a scripted function checking vehicles every few secs:

this is not a solution and this wont work for drowned vehicles as teh damage seems to be permanent

Cars fixed in 150293

vehicle engineon true; does not work, isEngineOn turns false after that.

Is this intended behaviour? Don't seems the case reading above

Any workaround? Depending on mission type it may not be so "minor" issue byt somewhat annoying

Any workaround?

both
veh setDamage 0
and
veh setHitpointDamage ["hitEngine", 0]

should now work

In T169734#2405319, @BIS_fnc_KK wrote:

Any workaround?

both
veh setDamage 0
and
veh setHitpointDamage ["hitEngine", 0]

should now work

In the RC you mean?

dev, don’t think it made it to rc