Using CTRL as a modifier is quite frequent, especially in EMACS. Since it is usually (and definitely on my Thinkpad) placed in a position that can cause “Eamcs Pinky”, one of possibilities is to remap CapsLock to another Ctrl. Following a recipe on Emacs Wiki, this is one possible way:
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setxkbmap -layout "$(setxkbmap -print | awk -F + '/xkb_symbols/ {print $2}')" -option ctrl:nocaps |