I've been searching for a macOS keyboard shortcut to insert a checkbox before an item. The only ones I found did not work for me. I finally had to create my own Text Replacement to do this.
Open System Settings. Search for Text Replacements. Click the button Text Replacements. Click the + sign. In the Replace field, type -[]. In the With field, type - [ ]. Then click Add. Then click Done.
Now, to add a checkbox in the markdown panel, type -[] (note the trailing space) and you'll get - [ ] . I could find no better way than this unfortunately. But it is faster than typing - [ ] outright.
No, and cmd-shift-9 does not work either.
I use Karabiner-Elements only to get Quit application by pressing command-q twice so I can avoid quitting with CMD-Q when I mistype CMD-W.
Some of those other tools look interesting but will require some time to set up and learn.
I prefer to use native solutions whenever possible instead of apps or browser extensions.
For example, the Eject key remapping example is much more easily done in System Settings->Keyboard shortcuts->App Shortcuts->All Applications->Sleep->ALT-CMD-F12 where F12 is in the same key position as EJECT on an Apple keyboard. This is for my much better Keychron keyboard.
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Under Linux and Windows It only works in the RTE editor and not in the markdown editor...
If the checkbox is not a part of a list you should be able to add it like a character (like in a text editor). You need to find its code number.
I think you can also use the character palette (control+command+Spacebar), search for ballot, and then double-click the character to insert ☐ into your Pages document.
If it's OK for you, use then a keyboard customizer (see previous post above) in order to link the shortcut of your choice to this symbol.
I think in Markdown it's the only solution...
Why not to click on the 
button in the menu? Sounds quicker to me.
If you want just to add the actual symbol - ☐, you can use replace text in settings like this:
or use any other abbreviation instead "chk" you like.
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