Consider an analogous situation. It doesn't matter whether a heart valve is made of biological material grown by the organism containing it or is made of plastic, as long as it behaves in the right way. One might express this by saying that its function is separable from its form. That doesn't mean that one is postulating function as some mysterious and ghostly entity which causes the physical object to perform (i.e. dualism). It's just that any physical object which performs the right way will do.
This is what is being claimed of uploading. Any physical object that performs the right way will be a mind, regardless of its physical constitution. Take any person, and a physical object that performs in the right way will be a copy of that person's mind. We know very little about what it takes to perform the right way, but we have no reason to suppose that what evolution came up with is the only possible physical substrate.
So is there any consideration in uploading thought given to subjective experience and it's relationship to the substrate? Certainly there is no reason to suppose that what evolution came up with is the only possible physical substrate I agree.
The International Journal of Machine Consciousness recently published its special issue on mind uploading. The papers are paywalled, but as the editor of the issue, Ben Goertzel has put together a page that links to the authors' preprints of the papers. Preprint versions are available for most of the papers.
Below is a copy of the preprint page as it was at the time that this post was made. Note though that I'll be away for a couple of days, and thus be unable to update this page if new links get added.