The difference is, that the SATA connector was made with Hotswapping in mind.
Which is better to connect to?
Depends on what you want to connect to it. If it´s your run of the mill harddrive you put into your computer and only remove it once it died, then i´d call it a tie. If you want nice, if you can spell "airflow" or if you need to swap your drives regularly, then the choice is quite obvious.
I´m really curious about your second question though. I´m not certain i fully understand what you are asking. 8O