Not certain if I understand you setup completely. Mostly because I don’t know most of the gear involved.
But in generally I recommend to set the keyboard mapping middle note to a value that is more or less the middle of the ranges of notes you intend to play.
The middle note will also map the scale root to a certain keyboard key, so this should be the same in other gear (motm). Otherwise you will play two scales with different root notes.
The actual tuning should be performed with a defined note played on both setups (G6 for example) until both setups have the same pitch.
following this both setups should track well – provided of course that the other CV interface has the same (or better) precision as µTune.
Hope this helps a bit