Just an FYI:
commands for scratch and journal note creation is registered as aliases to the lookup command with different arguments fed into them as default. this is causing the problem you are facing (i.e. "scratch" not showing in your keyboard shortcut list) because vscode sees all three commands as the same and is possibly hiding the other two.
I will be fixing these by actually adding separate commands for the other two, and registering them under a unique name so that it shows up correctly in the user-facing UI. (The two commands started off as a lookup-derivative feature back in the day and it's time for us to let them be independent 🙂) The change should be in for the upcoming week's release.
This doesn't fix your problem with conflicting keybindings, but that is unfortunately something we have to spend more time discussing. I have started a thread on this matter a while ago:
https://github.com/dendronhq/dendron/discussions/700
Feel free to add your thought here, but this is a very tricky subject that we as extension authors can't make changes lightly, so no solid ETA on when we could take action on this (especially when we are on an ecosystem where countless numbers of contributed extensions fight over the keybinding real estate)