We got 2 kit upgrades. Mark 2 can only be upgraded with a kit mark 2 kit upgrade or credits and mark 4 can only be upgraded with a mark 4 kit upgrade or Iridium.
The best ship is always the one, which have all mark 4 equipment, modules and weapon equipped.
Penalties remain the same as they are now and they do not mitigate in any way, for penalty specific equipment, which presents it.
Only mark 4 should provide such a special reward - an additional standard and free synergy bonus is increased by 10% overall for such standard ship/s only.
Ammunition and missiles do not count. All that counts, is a fully equipped and upgraded (only mark 4) standard (fully ranked) ship.
Bonuses do not stack with all 4 ship slots. Switching to another, different ship without such bonus, will not affect you.
Basically, this is a permanent 10% standard and free synergy boost, which does not stack or cancel, until one slot is unequipped or not matched with mark 4 equipment, modules or weapon.
Such ship is indicated with yellow star icon in the ship’s tree and in game’s screen.