I also have issues with custom modifier keys. Namely "spacebar". For instance if I have a hotkey assigned to "spacebar R". This doesn't work unless I have deactivated any hotkey that is using "R". The software doesn't register that "spacebar" is putting existing keys into a different modified state.

Offtopic
Another weird quirk is that "shift Right Mouse (view3d.cursor3d)" cannot be reassigned to any other hotkey and maintain its drag function. For instance if I assign view3d.cursor3d to "alt right mouse" I am unable to use the drag cursor functionality. Somewhat strangely, if you disable "shift right mouse for view3d.cursor3d" the hotkey still works no matter what. It's like the blender thinks this hotkey is so essential that there is no way to dispose of it or change it to something else.

I would love if the hotkey editor were completely transparent and didn't hide functionality from the user as I keep running into conflicts where blender acts like it can be completely customizable, but behind the scenes it's holding back.

That's strange, but it seems that is designed to work like this. See:
https://developer.blender.org/diffusion/B/browse/master/source/blender/windowmanager/intern/wm_event_system.c$2050-2052

/* Only keymap entry with keymodifier is checked,
 * means all keys without modifier get handled too. */
/* That is currently needed to make overlapping events work (when you press A - G fast or so). */

keymodifiers other than Ctrl, Shift, Alt, OSkey are not checked by keymaps without keymodifiers.
This causes the first keymap in the list (which in this case is the one with Left Mouse and without the Numpad Enter modifier) to be used.

A workaround is to move the keymap without the modifier to the bottom of the list (by deleting the keymap that has only Left Mouse and creating it again).

Thank you! This information was extremely helpful as I was mourning the loss of my spacebar modifier and though I think hotkey setup in blender should use modo as a template (including an easily comprehendable text file that you can edit hotkeys in) I'm happy to find that part of blender's lack of functionality was just my own lack of knowledge of how its hotkeys work.

In T68621#837961, @Germano Cavalcante (mano-wii) wrote:

A workaround is to move the keymap without the modifier to the bottom of the list (by deleting the keymap that has only Left Mouse and creating it again).

Hi Germano, hoping you might go into a bit more detail here? My confusion is such: If I create the following keymap Window > New File and I set it to F19 A then this will also trigger the "select all" command. But I can't put the new keymap above Object Mode > (De)select All because they are in separate branches of the keymap tree. Can you help make sense of how to implement the workaround? (is it even possible?)