I currently have a hydraulic handbrake fitted inline and it works great but I'm not so impressed with how it pushes back against the foot pedal. I have cables fitted to it to make it legal but they are mostly for show and I'm not sure they would do much if I had to use it as an emergency brake.

I was thinking about mounting another caliper on the rear uprights to have a completely independent system. Would that be legal? - or does one system have to be mechanical (or electrical).

Hand brakes should be mechanical

If the system was completely independat i.e. Seperate master cylinder and calipers I think yes.
Those with more mot experience may say otherwise.
I assume the hydraulic handbrake is for rally or auto testing

You're allowed a hydraulic system to assist in application/release of the parking brake, but the brake has to remain applied solely by mechanical means while applied, locking a master cylinder in position is still a hydraulic system and is not acceptable. Testing such a system may require a gradient test on top of the normal rbt/tapley test to ensure only the mechanical system is the source of brake effort.
If you have single circuit brakes, the handbrake performance also has to meet the balance and grab requirements.
A separate spot caliper applied by mechanical means on a separate lever would be perfectly acceptable as long as it met the appropriate efficency during the brake test.

Dave