Actually, that's not true, that is, custom shortcuts do not necessarily work.
To clarify: Shortcuts involving keys that differ on Dvorak and Sholes layout do not work when system keymap is set to Dvorak. So, for instance, alt+f4 works, as does ctrl+shift+m ('m' and 'a' are in the same position on both Dvorak and Sholes layout). The latter is probably where my confusion about custom shortcuts working arose from.
Actually, that's not true, that is, custom shortcuts do not necessarily work.
To clarify: Shortcuts involving keys that differ on Dvorak and Sholes layout do not work when system keymap is set to Dvorak. So, for instance, alt+f4 works, as does ctrl+shift+m ('m' and 'a' are in the same position on both Dvorak and Sholes layout). The latter is probably where my confusion about custom shortcuts working arose from.