I do not exactly understand why there should be a version mismatch as both kernels were compiled from the same source? But I must admit that I do not know much about how this version checking works exactly.
I'm not sure that I understand what you mean here. What happens if another package which requires a custom kernel config needs to be installed. Let's say a package that needs usbnet supported. Then the maintainer of this package needs to recompile hotspot-kernel with the addition of usbnet? And would the package on which it depends still be called hotspot-kernel? I don't think you should have a dependency to a certain kernel config. I've never seen it done anyway.