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Mark, I appreciate your willingness to help us out here. TBH, I don't feel that my situation is unique to submodules. It appears to me that the problem would arise anytime that you have a conflict of a file between what you have in your working copy, and what your trying to checkout. I'd love to be able to add some tests around this, but have been quite busy at work in other regards lately. My 2 cents are, do we really need clean after checkout? Is there any situation that this behavior is needed, that can't be taken care of by doing a clean before checkout? Perhaps we should change Clean After Checkout to be called Clean Before Checkout, and change its behavior to do what we implemented in clean before checkout? What do you think? I'm more than happy to have David or I help out here.
I should mention, what worked for us was the correct order of operations. We didn't need a git clean -ffdx, we just needed git clean -fdx and git reset --hard to be executed on all submodules BEFORE we do a checkout on those submodules.