It's not a complex genetic situation at all. Homozygous lethals are everywhere, even in mice. You can't disregard how genetics works, it's set in stone. I also don't understand where your point about recessive came from but that's a moot point.
The blackhead spider project isn't a waste genetically at all. It's not a waste to make super black heads nor is it a waste to make normal looking supers. The genes that make that normal looking snake, spider and black head, are still nice genes to have around and it's a super. Supers are always a welcome addition to my collection. It would also put to rest the super spider debate once and for all.
Also, technically everything in this hobby is anecdotal evidence but we've been able to accurately predict to a T what will happen when you put X and Y together and if XY is allelic or not based on, again, breedings. Imagine how amazed everyone was when the first allelic combo was made, which if I recall was the super stripe. No one would have known what was going on. It's through breeding and taking note of what comes out and using that information to predict what will happen with breedings, do we start to understand what is going on just as Gregor Mendel did many years ago.