I'm not aware of any way to batch process video in Premiere... since Photoshop does handle video (to a point) you might be able to set up some sort of a batch process there, but I'm not sure how you would do it... might be worth posing your question over in the Photoshop forum to see if any of the guys there have suggestions...
This sounds like a job for After Effects. Have you tried that?
Check to see if this works:
Create and Import your Matte into PrPro. Place it on the desired Video Track, and then extend its Duration for all Clips on that Timeline. Apply the Track Matte Keying to the first Clip, and make the attributes adjustments to it. Rt-click that Clip, and choose Copy. Then lasso all other Clips in that Track, Rt-click on them and choose Paste Attributes. Does that work?
PS - not sure if a Nested Sequence would also do what you want.