Hi Chipp - it's because Flow works on the "underlying surface" of the target surface, it shrinks down that surface to the UV bounding box of the trim curves, but it does not follow directly along trim curves, it follows the full surface beneath those trim curves.
When you do the boolean part, the surface that you are getting has trim curves on it that mark cut away areas.
You can get a better idea of what I'm talking about if you select the sphere part, then run ShrinkTrimmedSrf ( http://moi3d.com/3.0/docs/moi_command_reference10.htm#shrinktrimmedsrf) , then turn on control points for the sphere fragment by using Edit > Show pts - you will then see the control points for the full underlying surface, which extends a ways past the boundaries on 2 sides, and if you select the trim boundaries and hit delete to untrim it you'll see the full surface that Flow is using and how it's longer in one direction than the other direction.
When you use a surfacing command like Loft, Sweep, or Network, those all build untrimmed surfaces as compared to using a boolean which makes trimmed surfaces.
EDIT: looks like Burr beat me to it! :)
- Michael
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