The actual problem is not APFS but Apple's programs doing (and their advice to developers to do) normalization. It wouldn't be a problem if programs just used the file names given to them.

In fact, I think the normalization HFS+ does is more problematic. For example, fish shell can't complete file names when you use un-normalized characters in the input. [0][1]

Edit:

0: "Unicode normalization issues with HFS+" https://github.com/fish-shell/fish-shell/issues/474

1: "Completion does not work for special characters" https://github.com/fish-shell/fish-shell/issues/1794