[Guillaume86]

Have you tried https://atom.io/packages/keyboard-localization?

I used the auto keymap generation feature (you just type the caracters that have issues in a textbox and it generates/saves a keymap) and I don't have problems with my fr-FR keyboard anymore.

[ivoras]

Yes, it apparently fixes some problems for some layouts (notably, the German and French ones), but not for others (including my layout...).