How to use movie files in both Photos and iMovie without having duplicates?
Found this answer at Apple Discussion forums:

This works for me with Final Cut Pro (I think it'll work on iMovie too):    


Add the video to your Photos Library.
Head to your Pictures folder.
Perform a right click on 'Photos Library'.
Hit 'Show Package Contents'.
Go to 'Masters'.
Select the year, the month and the day the video was taken (you can easily check this in the Photos app by performing a right click on the video and then click 'Get Info').
Drag the specific video into the iMovie application to use it with iMovie.