Stock: yes, yes, and no. Ground clearance easily sorted out with moderate lift and better tires. The D90 comes stock with 32s but on a D1 32s would rub without some lift. Axels, easy upgrade, especially if you're adding lockers, you'd want those axels upgraded anyway. Deep water? Stock they both do about the same. You can push a bow wave in front your hood, so long as you keep moving. Adding a snorkel to either one will get you deeper than you'd like. D1 takes a little longer to dry out after getting water up over your seats. Plays hell with the CD changer too.
Don't get me wrong: D90 is very cool, I like the bare bones design and would love to own one, but you can get the same capability for less than half the cost with the D1. And the availability is greater.
Keep in mind though, owning a Rover (or any other vehicle built in the UK) requiers a commitment to learn how to maintain/ repair/ modify it yourself. Otherwise you'll go broke paying someone else to do the work. I learn something new every week ! They're also slow, have weird electrical gremlins in them, and generally prone to little failures, but the design is simple and pretty easy to fix when it breaks. I think a lot of people are disappointed with all the relaibility issues and street performance. These things are designed for off road use. If that's your intention, you won't be disappointed.
I think with most Rover owners it's a love/hate thing. It certainly is with me..