Get your clip positioned roughly where you want it, right-click on it and select Nest. Apply the Track Matte effect to the new nested clip/sequence. If you need to reposition the clip, double-click on it to open it in a new Timeline panel tab; you can move the clip there.
Premiere Pro's default rendering order is effects first, transformations second. By nesting the clip, you're forcing Pr to render the transformations first, and then the effects.
Thanks Colin, I did think about nesting sequences but I thought it wouldn't be as convenient as being able to manipulate the clip's zoom and position on the timeline. I did give it a try your way and it did work, but I find going back and forth between the 2 sequences is kind of hit or miss and almost as much trouble as just using the crop tool. Do you know of any other way that I might be able to get what I want but do it all on the timeline? I just want to decouple the motion paramenters from the matte.
I would imaging vignettes would have this issue as well?
Two cents added for free.... I think that you'll find that the more that you work with nested sequences, the quicker you will become at it and the more second nature the task will seem. It won't feel any more inconvenient than adjusting FXs in the control panel or other often repeated tasks. On plus side, the more that you train your editing brain to utilize nested sequences, many more possibilities in compositing and striking titles sequences will open up to you.
One of the basic tasks that I do repeatedly is create frames for cropped, resized, or lower resolution video clips using the Title Maker. It is a simple sequence with two tracks, video on lower and frame above. To make the frame, I just put the cropped, resized video on track one, then open the title maker and draw a box over the video, being sure to match the size neatly. Next, I add a stroke to the box then un-check the Fill Color attribute toggle of the box. That leaves the stroke as a frame. Then I adjust the stroke's attributes until it looks the way I want and then lay the title\frame over the video on the timeline. Done. To repeat the effect on another clip of the same size\proportion, I just duplicate the sequence in the project widow, rename it, then replace the video track in the sequence while keeping the frame intact. Any motion attributes can be copied and pasted.
Also, I create multi-track compositions with separately moving elements on a good portion of my lower 3rd title sequences this way. The results can be comparable to After Effects work.
Best of luck.