I personally don't mind the artwork bleeding over onto the spine per se, but in the case of Super Mario Bros USA at least, the layout of the front cover clearly looks better in your second example. I already thought things looked a little cramped in your first version, having this one to compare it to just makes it all the more apparent. Having said that I'm not against the design element itself, I think it looks neat and I don't mind it as long as the actual front cover doesn't suffer because of it.
I think spine colours based on the colours of the cartridges is an interesting idea in theory, but I'm not convinced that it's such a good one in practice. You're bound to come across games where the cartridge colour will clash with the design of the logo and/or the maroon and gold of the template itself. Either way I don't think the template necessarily has to dictate what the spine should look like. I don't think it'd be a big deal if there is no totally coherent look for the centre of the spines - There's still plenty of common design elements to tie covers together.
Another thing I'd like to mention is that the Famicom controller graphic on the back seems like it could be a bit more subdued, especially on the SMB2 cover. The relatively high contrast and intricate detail, combined with the small text make things look a little busy, and the text more difficult to read than it really should be. Again, I think the unique colours for each game is neat in theory, but I think for the sake of readability it would make sense to have a unified, easy on the eyes look for the background.