@mhalsharif: I'm currently not using any Apple hardware, but I'm seeing
all the same behavior you are (except I don't lose settings on
lock/unlock).

I have currently done the following things:
* I moved all my keyboard customizations from dconf settings 
[/org/gnome/desktop/input-sources/xkb-options] (which is where Tweak Tool puts 
the config) and put them in /etc/default/keyboard:XKBOPTIONS. Since these 
settings are default, when the keyboard resets to these defaults, it resets 
back to the config I want. (This fixes the keyboard reset, but still will not 
fix the mouse resetting issue.) If you want to try this approach, you can just 
add the default configuration options like this:
XKBOPTIONS="shift:both_capslock,ctrl:swap_lalt_lctl_lwin,caps:escape"

* I have also downgraded mutter (`sudo apt install
mutter=3.36.1-3ubuntu3 mutter-common=3.36.1-3ubuntu3
libmutter-6-0=3.36.1-3ubuntu3 gir1.2-mutter-6=3.36.1-3ubuntu3`). This
downgraded version fixes all the resetting issues (although I'm stuck on
the downgraded mutter version until a fix gets released).

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https://bugs.launchpad.net/bugs/1899206

Title:
  Tweaktool Keyboard “Additional Layout Options” not persisting on USB
  keyboard unplug/reconnect

Status in Mutter:
  Unknown
Status in mutter package in Ubuntu:
  Confirmed

Bug description:
  I am running Ubuntu 20.04.1 with Gnome. I am seeing new behavior which
  seems to have been introduced within the past couple of weeks. I have
  a couple custom keyboard settings configured in Tweaktool "Additional
  Layout Options". These settings work great.

  I have a USB keyboard plugged into the machine. If I have the keyboard
  plugged in when I start my Gnome session, the customized keyboard
  layout options are correctly applied to the USB keyboard. If I unplug
  and reconnect the keyboard, the keyboard does will _NOT_ have the
  customized keyboard settings.

  If I restart my Gnome session (using Alt-F2 -> "r"), the customized
  settings are applied to the keyboard.

  I think this behavior is something new. Before, I was able to
  unplug/reconnect my keyboard and it would apply my customized keyboard
  settings on reconnect. Is there anything I can do to force the
  application of the custom keyboard tweaks on USB keyboard reconnect?

  Is anyone else able to reproduce this? I don't have any other machines
  with Ubuntu 20.04.1 to test with.

  Thanks!

  (This is also cross-posted at askubuntu:
  https://askubuntu.com/questions/1281162/tweaktool-keyboard-additional-
  layout-options-not-working)

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