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.
We don't know how subjective experience arises, so the hope would be that simply modelling all the physical stuff that we can find will be enough to capture that process, whatever it is. A photocopier doesn't need to understand what it's copying.
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.