Some background: we decided to adopt C4 as middle C because that’s the standard used in MusicXML, the MIDI file standard (see the spec) , scientific pitch notation (see https://en.wikipedia.org/wiki/C_(musical_note) ), and Sibelius, among many others.
Unfortunately though, Cubase, HALion and many VST plugins have adopted the C3 standard. Some apps seem to adopt the C5 standard.
This isn’t ideal. Hopefully we can mitigate some of it in the future by offering a preference. We’ve added MIDI learn buttons next to some of the controls that specify MIDI pitches so that you can just hit the keyboard, which is then unambiguous.