So in X-Wing, the FA T-70 X-Wing comes with an upgrade that says X-Wing Only. Which allows both the original and the T-70 to use it. MkII Ion engines do the same for TIE ships. Not specifying an individual ship, but a class, or design base.
The same could be done for the Neb. They could release another Nebulon series of ship, such as the B2, D or K, which could come with some Nebulon only upgrades.
Such as, oh, I don't know
Reinforced Lateral Projectors
Modification
Nebulon Only
Increase the shield rating of your left and right hull zones by 1
You gain a redirect defence token
Modular Weapons Bay
Nebulon Only
Your upgrade bar gains the (offensive retrofit)
Enhanced Operations Centre
Nebulon Only
Your upgrade bar gains the (weapons team)