Can confirm. I also tried to manually invoke the setting:

$ gsettings set org.gnome.desktop.input-sources xkb-options
"['ctrl:nocaps']"

Doesn't work, too. My current workaround is using setxkbmap directly:

$ setxkbmap -option ctrl:nocaps

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Packages, which is subscribed to linux in Ubuntu.
https://bugs.launchpad.net/bugs/1903483

Title:
  "Caps Lock is also a Ctrl" setting stops working when connecting an
  external keyboard

Status in linux package in Ubuntu:
  Confirmed

Bug description:
  In Tweaks, I've set the "Caps Lock is also a Ctrl" setting.  However,
  when I connect my external keyboard via USB, the setting stops taking
  effect.  If I go to Tweaks, the setting still appears to be enabled,
  but I have to disable it and re-enable it to make it take effect
  again.

  ProblemType: Bug
  DistroRelease: Ubuntu 20.04
  Package: linux-image-5.4.0-52-generic 5.4.0-52.57
  ProcVersionSignature: Ubuntu 5.4.0-52.57-generic 5.4.65
  Uname: Linux 5.4.0-52-generic x86_64
  NonfreeKernelModules: nvidia_modeset nvidia
  ApportVersion: 2.20.11-0ubuntu27.11
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  mgummelt   2175 F.... pulseaudio
   /dev/snd/pcmC1D7p:   mgummelt   2175 F...m pulseaudio
   /dev/snd/controlC0:  mgummelt   2175 F.... pulseaudio
  CasperMD5CheckResult: skip
  CurrentDesktop: ubuntu:GNOME
  Date: Sun Nov  8 21:15:48 2020
  HibernationDevice: RESUME=UUID=b92322bb-a24e-4286-8452-f6e2272a4fb3
  InstallationDate: Installed on 2018-03-26 (959 days ago)
  InstallationMedia: Ubuntu 17.10 "Artful Aardvark" - Release amd64 (20180105.1)
  MachineType: LENOVO 20ENCTO1WW
  ProcEnviron:
   TERM=xterm-256color
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcFB: 0 i915drmfb
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-5.4.0-52-generic 
root=UUID=ab4a36d6-e419-424e-9f0d-3635cd2543b5 ro quiet splash vt.handoff=7
  RelatedPackageVersions:
   linux-restricted-modules-5.4.0-52-generic N/A
   linux-backports-modules-5.4.0-52-generic  N/A
   linux-firmware                            1.187.3
  SourcePackage: linux
  UpgradeStatus: Upgraded to focal on 2020-07-09 (122 days ago)
  WifiSyslog:
   
  dmi.bios.date: 08/28/2019
  dmi.bios.vendor: LENOVO
  dmi.bios.version: N1EET86W (1.59 )
  dmi.board.asset.tag: Not Available
  dmi.board.name: 20ENCTO1WW
  dmi.board.vendor: LENOVO
  dmi.board.version: SDK0J40697 WIN
  dmi.chassis.asset.tag: No Asset Information
  dmi.chassis.type: 10
  dmi.chassis.vendor: LENOVO
  dmi.chassis.version: None
  dmi.modalias: 
dmi:bvnLENOVO:bvrN1EET86W(1.59):bd08/28/2019:svnLENOVO:pn20ENCTO1WW:pvrThinkPadP50:rvnLENOVO:rn20ENCTO1WW:rvrSDK0J40697WIN:cvnLENOVO:ct10:cvrNone:
  dmi.product.family: ThinkPad P50
  dmi.product.name: 20ENCTO1WW
  dmi.product.sku: LENOVO_MT_20EN_BU_Think_FM_ThinkPad P50
  dmi.product.version: ThinkPad P50
  dmi.sys.vendor: LENOVO

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