Sure, that would work. You don’t necessarily need to define a pieces palette or even a map in the main module. You could simply use it to define piece behavior, traits, prototypes, toolbar buttons, and any other things the scenarios have in common. Then each extension could include its own palette, at-start stacks, and map windows for the scenario.
However, it sounds like it might be a good idea to define a pieces palette in the main module anyway, including ALL the pieces, and then create the At-Start Stacks from that palette when you build the extension. This way you’re not building and re-building a new palette in each extension like you are now. You could even define the palette as Hidden and use it to build your At-Start Stacks in the editor. Only the person editing the module would be able to see the palette. To the players, they’d just begin the game with the At-Start Stacks visible.