300 years ago they were using the same ranks. Were they not?
Open to debate, but the Royal Navy had a rank structure fairly similar in place for higher ranks. Junior officer ranks have evolved a good deal over the last 300 years, but on the other hand, it could be argued that they were more "formalized" then "evolved."
Exactly, its all in the interest of maintaining a disciplined, cohesive, effective unit. If the ranks didn't change much (There is the notable absence of many modern officer ranks in FS2, it is possible these are in place of longer minimum periods of service in the GTVA ranks), it is evident that the rank system works. The GTVA (possibly) eliminated many of the 20th-21st Century Officer Ranks in the interest of streamlining the system. This helps when orders are passed down the ranks, this would most likely be highly effective in ships such as the Colossus, in which there are increasingly large numbers of hands aboard as many important orders have a much simpler filtering process and with the amount of Officers required to staff many GTVA Capital Ships, it simply isn't practical to have to account for over nine different levels of authority on the bridge. A more streamlined rank structure such as the GTVA's also helps to prevent a top heavy chain of command, but rather equalises ranks, as after the rank of Lieutenant, the number of people occupying ranks above should (logically) be dramatically lower, as ranks such as Flying Officer and Sub-Lieutenant present in Modern Navies are folded into the Ensign, LtJG and Lt ranks