Kinto swaps the keys the way you want, and I am the author of it. https://github.com/rbreaves/kinto
On this example below it is from when I was mapping the Cmd location to Super while under the terminal - and to avoid writing custom xkb files. Kinto actually does use Ctrl+Shift in the Cmd key location for the terminals now.. but I use some custom symbols and types files for setxkbmap and xkbcomp to accomplish it.. again too much to post here and have it all make sense, because you'd still need the rest of my code to have it run right any ways.
# permanent apple keyboard keyswap
echo "options hid_apple swap_opt_cmd=1" | sudo tee -a /etc/modprobe.d/hid_apple.conf
update-initramfs -u -k all
# Temporary & instant apple keyboard keyswap
echo '1' | sudo tee -a /sys/module/hid_apple/parameters/swap_opt_cmd
# Windows and Mac keyboards - GUI (Physical Alt is Ctrl, Physical Super is Alt, Physical Ctrl is Super)
setxkbmap -option;setxkbmap -option altwin:ctrl_alt_win
# Windows and Mac keyboards - Terminal Apps (Physical Alt is Super, Physical Super is Alt, Physical Ctrl is Ctrl)
setxkbmap -option;setxkbmap -option altwin:swap_alt_win
# If the hid_apple driver is not loaded for Apple keyboards, which can be found out
# by the lsmod command then the above setxkbmap commands will not work
# Use the following commands for Apple style keyboards without an hid_apple driver
# Note: this could also apply to hid_apple driver as well
# if this option is set to 0 inside swap_opt_cmd
lsmod | grep hid_apple
# Apple keyboard without hid_apple - GUI
setxkbmap -option;setxkbmap -option ctrl:swap_lwin_lctl,ctrl:swap_rwin_rctl
# Apple keyboard without hid_apple - Terminal
setxkbmap -option;setxkbmap -option altwin:alt_super_win
# If you want a systemd service and bash script to help toggle between
# GUI and Terminal applications then look at project Kinto.
# Note: The above may not work for Chromebooks running Linux, please look
# at project Kinto for that.
# If anyone would like to contribute to the project then please do!