What you are describing in terms of mechanics are essentially a "brawler" ship and a "support" ship. The flagship is very unique. Every faction's flagship is different.
You aren't wrong that the brawler and support ships are similar, but they do have notable differences in their ability to kill, survive, and maneuver. One big thing to take account of is the location of their components. A big part of this game is disabling an enemy's potential to move/shoot. Take advantage of each faction's component location and capatilize.
Other than that, they do have similar fighting styles.