Why are askubuntu.com and meta.askubuntu.com considered as same Stack Exchange site (Same Reputation points on both site), while stackoverflow.com and meta.stackoverflow.com are considered as different sites (Different Reputation points on both sites)
Because MSO is special. It was the first meta site and handles all the suggestions and bugs for the entire SE network, not just SO.
I think if they had the choice to start over, they'd probably make it rep-free like the rest of SE's metas but there you go. There's no going back without annoying a load of people.