Well, there's no "should" or "shouldn't" about it, it's just the way it is.
The manual for zip says, "... paths stored in zip archives are always relative." Zip actually is deliberately programmed that way.
You could get the zip source code and modify it to add a new option to specify the starting directory. But that would be an awful lot of work!
Do you have to use zip? Would tar + bzip2 do? If so, you can do it in one command with tar's --directory and --bzip2 options.
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