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I have installed Stylish 0.9.2 to my Thunderbird 52.5.2. When I press the [Settings] button, it says "Stylish not detected, please install/enable". But it IS installed and it IS enabled.
Which version of Stylish have you installed?
Stylish-Custom doesn't support webextensions (or the webextensions version of Stylish).
I'd recommend using v2.0.7