Actually it does make sense, but would be easier in the long run to just figure out how to add the repaints to the existing aircraft. keep in mind, you can change the name and have 100 copies of the super hornet in your FSX folder, but it will only display as one since it goes by the info in the aircraft CFG, which is where you add the additional info when you install a new paint.
Here is an example of the Acceleration F-18
just copy the original entry you have for your super hornet as many times as you have texture folders and then on each one, change the bold areas you see here to reflect each texture folder you have installed
[fltsim.XX] <-- corresponding number for each entry
title=FA-18 Hornet ( ) <--a specific name for each variant
sim=FA-18
model=
panel=
sound=
texture= <-------the name of the texture folder
kb_checklists=boeing_FA18_check
kb_reference=boeing_FA18_ref
atc_id=N001 <-- ATC number
atc_airline=NAVY
atc_flight_number=001
ui_manufacturer="Boeing"
ui_type="F/A-18"
ui_variation="Blue Angels 1" <-- variant, usually the same as in the title
ui_typerole="Twin Engine Jet"
ui_createdby="Microsoft Corporation"
description="The Hornet combines the ruggedness required of carrier-borne aircraft with speed and superior agility, especially at high angles of attack. Its powerful engines, canted vertical stabilizers, horizontal stabilators, large leading- and trailing-edge flaps, and sophisticated flight control system all contribute to a level of performance that makes the Hornet a versatile front-line fighter in several air forces around the world."