Yes, they are considered separate and leveled separately. Playing the more casual modes such as the Global Colosseo online will not count towards your online ranking, only ranked matches do. You can easily test this out yourself by playing a quick ranked match. After the fight is finished, you will gain a certain amount of online rank points based on the results of the match, the difference between both of your current ranks, etc.
As for your other questions - it is likely that the other people who have higher ranks than you but less wins merely played people who were significantly higher ranked than them, and won. For example, fighting someone who is A1 when you're E5 and winning is likely to reward more ranking points than if you were to get a win against someone who is the same rank as you.
For points awarded after a ranked match - unless you see points fill up your ranking meter (which should be done immediately following the conclusion of a fight), it is presumably separate from the points that rank you up.