The oem CRD arrangement is best, imo, but needs work, as you indicate - the required precipitate drain openings face the front of the vehicle, which allows the denser component free entrance - for proper maze operation, the openings should be in the lowest point of the rear wall or in the bottom wall, shielded from the front - air flow across\around the shield will provide a lower-pressure area behind the shield, which will aid precipitate drainage - normal air-flow leakage thru the openings aids in drainage
Other systems have a simple rubber drain valve, shaped like a flattened funnel - water is dense enough to pass the closed flap, air can get out, but not in
I'm not condemning the V6 system - Jeep didn't go cheaper on the CRD system, as is popular belief - they provided the most direct path of high-volume cooler air from the high-pressure area in front of the radiator bulkhead, but something got lost in translation\realization of air-maze technology, imo - or, maybe it was just too restrictive at high Boost levels - as you may have surmised, they didn't consult with me, on that.
For inclement weather\high water conditions, the snorkeled path to the higher position just under the hood is likely best - even so in extremely dusty conditions - the higher you can place the intake inlet, the better the results - the external snorkel tube used by the military and copied by the a\m crowd makes that statement - but, it is also severely flow-limiting, meant for fording streams at low speed\low rpm, and convoying in dusty desert conditions at low speeds - it's workable, but limiting.
Your 2.8L 173cuin engine pumps ~200 naturally-aspirated cfm at 3600rpm - it pumps ~100cfm at 1800rpm - ~50cfm at 900rpm
Roughly estimating, that's 400cfm at 3600rpm at 15psi Boost, 600cfm at 30psi Boost
The 3.7L 225cuin engine does similar, but will never exceed the naturally-aspirated flowrates - it will always pump ~200cfm at 3600rpm, written in stone = it has no turbine-driven compressor to increase those flowrates - 1Bar in = 1Bar out, ad infinitum - at 7200rpm it will only pump ~400cfm - I think 7200rpm was not part of the engine's original design specs, however.
The CRD intake was planned for high-volume turbo-service - the 3.7L intake was planned for low-volume non-turbo service - best to check it out completely, imo.