I am sure that if your shield projected inside of the ship, the ship will be cut in twain from the shields. That is not cool, especially if you cut crew members in half - that would leave a big mess and I hate dealing with messes.
...or the thin mitigation shield that covers the hull would prevent the shield from going in side the ship and therefore would just have a hole in it. Mitigation persists when the shields are depleted so I think that would win.
Actually.... I wonder if the ship models are whats off, not the shields. I notice that turning the camera around them doesn't behave as I'd expect. The Advent Loyalist Titan is a hair off as well, if I remember correctly.