This happens in both marginnote 3 and MNExplor. So each time I have to change font size of notes in SETTINGS in order to maintain font size of EXPORTED PDF.
Eg:
PDF of Note 1 - normal font size
PDF of Note 2 - normal font size
PDF of Note 3 - increased font size
I reduce font size in settings to maintain font size of PDF ➝
PDF of Note 4 - normal font size
PDF of Note 5 - decreased font size
The cycle continues