Unlike the original ToneDexter, all WaveMaps are normalized to the same sound power level. This means that the exact levels of the pickup and mic during training are not critical.
The reason bypass can sound louder is because the direct pickup frequency content is different than with the WaveMap, and our ears are more sensitive to some frequencies than to others. The input gain can of course be adjusted, but the difference in perceived level will still remain.
In software version 1.2 and above there is a provision to trim the WaveMap gain which will eliminate this concern. Tap the WaveMap button, the adjust the WaveMap trim control.
Starting in version 2.6, the loudness matching has been greatly improved. The trim control is still present, but you may not need to use it.