I understand that the reader mode is intended to be a cluster free mode that allows for better reading of a webpage and because of that there is no way (as of currently) to enable extensions in this mode, but there are extensions that I simply can't browse the web without, even in reader mode.
I have been using Vimium for a while now and losing my custom keybinding every time I enable reader mode is definitely not great.
In my case it falls into a inconvenience but it is not hard to imagine worse cases such as people who would like to translate the text using a extension or find grammatical errors for some reason.
Now it is obvious that some extensions are undesired in this mode and would even disrupt the website by modifying elements when it shouldn't, so my proposal is that we have an option in the extension "Manage Extension" page that should be disabled by default that allows to "Enable extension in reader mode".
Reader mode is much like a normal website, it has HTML, CSS and JS such as any other website so I don't see why this wouldn't had been possible from the start.