I would think the most elegant solution to the vignetting would involve the least amount of work, and have the least potential for image degradation. Software fixes seem to involve the most work and in some circumstances introduce the highest potential for image degradation. A center filter would probably stay on the lens; just shoot the scene, then you don't have to spend time correcting for the vignetting: the fastest and simplest approach.
Single Capture:
I spoke with Rod Klukas, the US ARCA Swiss rep today, and he described the manufacturing of the Rodenstock center filters - extremely time consuming, exacting, using special glass, diamond cutters, etc. He assured me that these filters ($1,500 for the 32mmHR CF) introduce very little if any image degradation. (They better not for that price!) He also stated that correcting for vignetting with software definitely introduces more artifact than using the filter. So if my logic is accurate, the only disadvantage to using the center filter is the longer exposure time. So if the wind won't let up, shoot the scene without the CF, and correct with software. From my experience though, I usually wait for minimum wind even when I've never had a need for a center filter - it's just something we do anyway.
I should also mention that Rod said that several of his customers with the 35mm & 32mm that ordered the CF were very happy with them - he didn't mention a flare issue or reduced contrast. He also said that the CF creates a "far more even tonality" than with using software. I have since asked Rod about the contrast question: in general, the Rodenstock CF's do not reduce contrast. An exception might be if you had your brightest part of your scene in the very center of your image, in that case the contrast might be affected regionally to a small degree, but the filter does not introduce a global contrast reduction. As far as flare, he suggested using a lens shade, whether or not you're using a CF. Using a CF doesn't increase the chance of flare on it's own; the wides are prone to it anyway.
Mutliple capture for stitching:
If you are going to shift a 32mm or other wide angle lens for stitching purposes, then you exaggerate the illumination gradient along the sagittal plane from center to corner, because you're moving towards the darker region of the image circle. The larger the gradient. the more is required of the LCC and possibly introduce more artifact. With the center filter, you lessen the gradient along that line, making the LCC work less. C1 is a great program, but as with any processing program, the more you "lean" on it, the better the chances of introducing artifact.
Summary:
If there is no evidence that CF's damage image quality, then there is little rationale for not using them; provided you can live with the longer exposure times, and expense!