I've seen one reference of this in comments a few months ago, but no other mentions. It seems that the "_Force-Quit_" shortcut is disabled when K-E is active.
I'm using version 0.91.2, remapping my Caps-Lock key to a Hyper key, on a 2016MBP 15" with touch bar running Sierra 10.12.5
This shortcut is working for me with Karabiner Elements 0.91.3, macOS 10.12.5, 2013 MBP 15". Caps-Lock is set as hyper key if used with any other key and as caps-lock if alone.
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Still exists on my computer
Karabiner version 12.1.0
macOS version 10.13.6
Sorry my fault. I need to check touchbar in device menu.
@RoadToDream were you able to fix this? I'm having the same issue.
@jm3 I didn't fix it cause it is not a bug at all. You need to check both the items listed in the "Devices" sub-table. See below

As touch bar is recognized as a secondary keyboard, you need to make sure it is set to respond to Karabiner's manipulation.
@tekezo could we re-open that issue, as it is not fixed yet?
Most helpful comment
@jm3 I didn't fix it cause it is not a bug at all. You need to check both the items listed in the "Devices" sub-table. See below

As touch bar is recognized as a secondary keyboard, you need to make sure it is set to respond to Karabiner's manipulation.