It's been a couple of years since I've used RED. Things have likely changed since then but I recall that when using the plug-in (not the Red Engine) it was necessary to delete a composition's background track in the BORIS timeline in order to achieve transparency in the Premier timeline. There may be others on here who are far more up to speed on this stuff - you might also get better information from BORIS support or BORIS forums, if they run any.

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