For a rectangular collar and an oval mast configuration we usually design Waterboot on the large side. We intentionally leave extra material that will fit over the corners of the rectangular collar. The extra material can be easily trimmed off after the Waterboot is installed and the bottom is adequately sealed by means of tape, hose clamp etc. Be aware that there will more than likely be soft creases on the Waterboot material as it wraps around the corners. This doesn’t affect performance but the look is just not as seamless as an oval mast and deck configuration.
Here is a PDF version of the Special Installation Instructions for rectangular and other non-oval mast/deck configurations.