Yes there is a reason: Most modern bikes that come equipped with disks do not have mounts for rim brakes. And many wheels on modern disk-equipped bikes do not have a brake track. Ofher than likely being impossible, it is entirely possible.

This is the only real trooublesome thing here - the disk/rim compatibility issue.

Many Surly bikes have rim/disk brake mounts. I inmmediately thought of the Karate monkey when I read the post. THe only issue might be fit for a tall rider. I am 6'4" and from studying the KM specs I think it might be a little small for me - but I like big fitting bikes. Surly also recommends against using rear disk brakes and a rear rack at the same time... although front disks and rear rim brakes are usually enough.

THe other option (and it is a good option since you have a decent budget to work with) is going with a custom frame. They will put whatever gadgets and nick-knacks on that wish. ANd you can be guaranteed a bike that fits. I have dealt with a lot of tall people buying bikes and there are a lot of people riding around on bikes that are too small. This could be the first time you ever ride a bike that fits!

Another bike that might work:
Kona Unit (but has no rack mounts or rim brake mounts but fit should be good);
Soma 29" MTB (but again, size might be an issue)

Edit:

I just read the OP last statement about not wanting to go custom - why not? It really is the best way to go. You could get a custom frame with everything you want that FITS, slap on a component set off a budget 29er mtb and seel the cheap frame and have the most kickass unique bike around! If I were you I would not be trying to avoid going custom but looking to convince myself or my financial manager that it is necessary. Sorry, buddy, but not many manufacturers are making frames for guys your size, and it is very unlikely that you'll find one that meets all yor strict conditions and have a decent fit.

Have you got a bike now?