I only recently learned what this is actually referring to, after scouring archive.org for Spanish, French, and German language versions of Lingua Latina per se Illustrata. Twain is being perfectly literal, though these days we'd narrow the debate to typeface as people rarely handwrite these days. Example: https://archive.org/details/erstesdeutsches00wormgoog/page/n... When first opening that book, I was like, "what kind of inanity is this!?" The same author wrote Spanish and French versions of that book, but both were printed using a perfectly familiar Latin typeface. After reading about the issue, I can sort of appreciate why that typeface was chosen, though it definitely steepens the learning curve.

There was a centuries long debate in Germany (and Germanic lands) over this issue. See https://en.wikipedia.org/wiki/Antiqua%E2%80%93Fraktur_disput... for info about the debate over typeface specifically. TL;DR: The Nazis resolved the dispute by fiat, in an odd twist of history settling on the Latin typeface.

(For typeface enthusiasts, I apologize for any poor use of terminology.)