Okay, so I took a quick look at my rain tray area. I see a couple of issues:
1. That's where the intake for the heater is... One would have to remove the elevated screen assembly to make room for the engine air filter. Maybe one could reconfigure it so it wasn't so elevated, but then you'd have to make sure to keep your rain tray drains good and clear of leaves. Either way, it looks like there is less room for an engine air filter in a Mk 2 than in your Mk 1 photos.
2. I have an A/C car, and the hard lines run along the firewall at the upper edge of the tray - leaves less room to cut a hole below them while still being in the tray sheetmetal and not in the passenger compartment (if that makes sense).
I do see that the plastic tray does a good job of shielding out water from above. One would only have to worry about a flood from below. Although, come to think of it, once you cut a hole to let the air duct through, you've just made another huge drain...
