Road frame VS. Cyclo-Cross frame Geometry
My knees are in agony. I ride a mtn bike on the road. I have my seatpost as high as I feel safe putting it. I know mtn bikes have a higher bottom bracket than road bikes. I don't know how cyclo-cross bikes compare. Are they the same as road frames? Or middle Earth of road and mtn frames?
They are supposed to be higher than road frames, but its simple enough to compare the geometry charts from manufacturers.
Your riding position is not dependant on the BB height. You can use the same saddle height on road and MTB.
NB since MTBS often use longer cranks, measure from the pedals, not the centre of the bottom bracket.
What do you knees have to do with it? A properly set up mtb shouldn't be bad for you knees. Or is the frame to small and you can't get the seat high enough?
My handle bars were about 5" below my seat on my mtb commuter. That is a bigger drop that I have now between my seat and the hoods on my cyclocross bike.
If anything a mtb will give you more options to ride lower gears at higher cadence and hurt you knees less.
I had the same problem on my MTB commuter, so I got a new seatpost and the problem was solved, but it took 6 months of daily riding for the pain and the problem to become apparent. Get a tape measure and do the fit calculator from... I cant remember where, but if you search the threads you will find it. It will probably help a whole lot.