Yes adding the effect is forcing fixed resolution to the group containing the effect. You can tell by the box around the group icon. Try applying it to each of the videos individually instead.
My bad, the same filters in Final Cut Pro X do have color mask and shape mask option. But just duplicate the clip, mask the duplicate, and mask that either with a shape mask or a luma key.
What export settings did you use? I’d export using h.264 if you want to start with a smaller file size – it will be recompressed but should still be ok.
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Mark Spencer
Freelance Producer/Editor/Motion Graphics Artist
Apple-certified Master Trainer
Author, Motion 4 from Peachpit Press https://www.applemotion.net
You need to place it in the Library in the Finder: User > Library > Application Support > Motion > Library Shapes, and then it will appear in the Shapes category in Motion’s Library.
Mark
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Mark Spencer
Freelance Producer/Editor/Motion Graphics Artist
Apple-certified Master Trainer
Author, Motion 4 from Peachpit Press https://www.applemotion.net