There are various factors to contribute while going under water..
1. Axle breathers - You can easily raise these as high as you want with more tubing
2. Air Intake - On a DII it is right above the front, drivers wheel well. Snorkel will raise this to the roof line
3. Engine - While it's sealed rather well, pushing it completly underwater for a while probably isn't good for it. The same goes for other areas, such as the transmission, transfer case, etc.. while they are sealed, water may be able to find its way through drain plugs.
4. Exhaust - Most likely not a problem since its pushing air out, but if you stall under water, then start up again, you can ingest water.. not good.
5. Electronics - This is where the real pisser is.. you can soak your transmission ECU, your main ECU, your fuse box, etc.. you can fix this by using rubbermaid containers and sealing them up rather well. For all the connectors, use some dielectric grease on them, it wont let the water in.
Those are all the major concerns, if everything is properly sealed, I don't see any reason why a rover can't go up to the snorkel/breather lines under water.. the main concern is #3 (engine/drain plugs/etc..)
As for a J**p, i've seen many of jeeps suck down water and kill their transmissions.. From what I understand, the inspection plate on the bellhousing unit will let a ton of water in since there is a drain hole there to let the water out. On some jeeps I think it's worse then others.. You have to modify the vent to raise it.
All in all, if you're going to be submerging something, get a diesel! The less electronics allow it to be submerged longer.