Same issue here. Firstly, this extension occurs from either Firefox or Chrome browser extension.
This is the expected behaviour:
This popup should appear.
However, this doesn't work.
Currently, the workaround is visiting the Yomichan extension settings and toggling "Use native window instead of embedded popup" -- which is what no one uses (takes too much screenspace)
In Yomichan:
Window section
Use a native browser window instead of an embedded popup (checked)
Perhaps this is a permissions issue?
There is a similar Safari/webkit extension called Safarikai which does the same thing (but is worse/less feature rich than Yomichan).
There's also other features on Yomichan not yet tested, such as use Local Storage, that may not work as well.
This extension is probably the #1 reason (apart from compact tabs) that I haven't tried using Orion as a daily driver.