Double tapping "A" will serve the same function as "ALT-A"
You can actually change it back to the default behavior. There is a handy shortcut for this "Select All Toggles", but it gets removed once you save a new preset.
EDIT: I discovered a workaround that gives me the best of both worlds. :-) Switch back to the Blender default config (and the missing settings will show). Activate your settings from that menu, then save a custom preset. If you need to make any changes (such as turning on extra shading options in the pie menu), switch back to the Blender default config, change the settings, then save a new (or overwrite) a custom preset. Works perfectly! :-)