E.g. 'A' followed by 'n' could have one ligature that looks like "An", and 'A' followed by 't' could have another ligature that looks like "At" where the A part is different (and the 't' too, of course).
Edit: here's an article about the concept: https://terrianncreative.com/using-ligatures-to-enhance-hand...
Edit: that is an amazing website btw, thanks for sharing :)
https://archive.org/details/JenkinsArtOfWriting/page/n25/mod...
(page 26 in the built in browser, plate 33 in the book)
Have the human write down not 1 but 50 times the font to be scanned and create 50 fonts.
Then pick one of these 50 fonts at random for each character.
I'd say that'd be the absolute simplest way (although not the most bandwith efficient).