I don't see why it wouldn't work to paint it with the bedliner paint. Read the paint directions carefully though - if a primer is required make sure you use the correct type. A friend of mine primed a car of his before sending it to a paint shop in order to save money, only to find out the primer was not right when his new paint job started alligatoring in spots less than a year later.
? Also make sure to tape off the openings well, etc.

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