Heyo. So I use the Dvorak keyboard layout for typing, but I’ll occasionally switch to QWERTY for some things. I set the keyboard to Dvorak by default during OS setup, but after my first reboot, it mysteriously changed to QWERTY… and only QWERTY.
I went into the System Settings app, and noticed that 1) the Dvorak keyboard layout mysteriously vanished from the settings, 2) my main shortcut for switching layouts (both Ctrls together) wasn’t set. I set them back up, but sure enough, next time I logged in, my system only had QWERTY for typing. (Though thankfully, my shortcut for switching layouts stuck.)
After a little more digging, I noticed something: the settings app actually has TWO sections for layout settings: “Keyboard” and “Input Method”
After some finagling under the Input Method pane, I managed to at least get it to default to Dvorak whenever I log in. However, setting keystrokes under Input Method seems clunky at best, and they keystrokes don’t even seem to work.
This said, I noticed that changing my settings under Input Method seemed to overwrite my settings under Keyboard - now instead of only showing the QWERTY layout, it only shows Dvorak. Whenever I do want to switch to QWERTY, I have to manually re-add it every time I log back in (and I checked: it resets with logout/login, not reboot). That said, the both-ctrls keystroke actually works.
I’m not 100% certain since the only other posts I found on related issues seem old and I don’t know what changes have been made, but I think this might’ve caused confusion for others… but nobody else noticed the redundant settings panes. 
I haven’t bothered trying a command-line workaround yet. It kinda seems like Dragonized Garuda is supposed to use the Keyboard pane (and honestly, it’s the one I prefer), but for some reason the Input Method pane is still in there and causing some problems. I haven’t checked if there are any features Input Method has that Keyboard is missing.
(Also, trying to refer to both by name is confusing. )
I can stick with re-adding QWERTY whenever I need it, for now. (That said, I noticed dictation software can get confused by having two input methods set up. Namely nerd-dictation, if it matters - I haven’t tried others yet.) What I particularly want to ask is: Can we please have just a single settings pane for keyboard/input settings? Preferably the Keyboard one?