The SE should be able to use the drive with an interleave ratio that accommodates the Plus, it will just be a bit slower(on the SE) than if using the best interleave ratio for the SE.

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A bit slower!? That's relative. And on an SE, who wants it slower? I would format the drive for the Mac you're using it on. Definitely don't format it on the SE for use on the Plus as it will be really slow, and may be contributing to your startup problem.