Is this still an issue?

you hover over a skill with mouse and press an f-key to assign it to shortcuts. TutorialTom even explains this.

(since 2014) Npc:says(_"You can also assign quick-select keys to programs. Simply hover over the program in the Skills/Program menu and press one of the keys [b]F5[/b] to [b]F12[/b]. Then, whenever you press this button, you will select the corresponding program.")

(also since 2014)   { N_("activate_program0"), SDLK_F5, KMOD_NONE },