One way to approach this, from a design standpoint, is to make additional rules modular and allow GMs to use them or not as necessary.
As an example, I'm adding rules for PCs joining factions to my current SD project. I'm not going to fold that in to any existing rules but rather make it a separate sheet and rules. This will separate form the faction rules themselves because some games simply don't need the PCs to be able to join factions.
Shadowdark is an elegantly designed game. I try to not obscure that core elegance whenever possible.