I think you're on a good track. Here's what you could do to get set up...
1. On the ground, compose a scene with desired shift
2. Use handheld spot meter for the brightest highlights you want to preserve
3. Enable highlight alert on your camera
4. Make several captures starting with +1 (relative to your meter reading) and increasing to +2 or more (overexposed)
5. When highlight alert warns you, back off as necessary
6. Look at the results in post-production
7. Make note of how many stops over the handheld meter's reading you actually just save those important highlights.
In doing the above just once, you have roughly calibrated your meter to your sensor's ability to preserve highlights. Once in the air, and on subsequent shoots, you can confidently expose to the right with only a single meter reading before you start shooting, maximizing your image quality for all captures of a particular scene. Simply meter the must-save highlights and open up the number of stops determined in #7 above. You will not be relying on the camera's meter confused by your shifted lens, and you can always take a quick look for your blinking highlights to confirm.
Alternately, if you have no other need for the handheld meter, you can just use the highlight blinkies to establish exposure.