The Giants get special treatment because they're the Giants. It's so hard to decide how to write team names because they're the exception to the rule. For example, saying "Yokohama vs. Chunichi" for yesterday's Game of the Week is natural. But "Hiroshima vs. Giants" just doesn't sound right, because one is using the location name for one and the mascot name for the other.
In the Pacific League one wouldn't say Fukuoka vs. Osaka, either, despite teams trying to identify more with their communities. And using the city name actually would work in the Pacific League since all of the teams are actually in different cities. (The Central League has both Yakult and the Giants in Tokyo.)
As for how the teams are used by their corporations, look around the site, this has been brought up a number of times.
This is a site about Pro Yakyu (Japanese Baseball), not about who the next player to go over to MLB is. It's a community of Pro Yakyu fans who have come together to share their knowledge and opinions with the world. It's a place to follow teams and individuals playing baseball in Japan (and Asia), and to learn about Japanese (and Asian) culture through baseball.
It is my sincere hope that once you learn a bit about what we're about here that you will join the community of contributors.
Michael Westbay
(aka westbaystars)
Founder
Any books or other web sites that can help would be a big help, too.