The tap tempo on the stompboxes is really designed for syncing up delays and modulation to the beat, and for this reason does not offer special accuracy. 0.5 seconds in 10 minutes is better than 0.08%, so it's not all bad. This is plenty good enough for most purposes and cannot easily be improved.

The MIDIclock output is timed by the internal crystal, not the mains frequency. Because there are only 24 MIDIclocks per quarter note, it is hard to get high accuracy. For this reason, a calibration setting would not be helpful.

If you need greater long term accuracy, as it appears you do, you should consider an external precision source.