I bought Sins at this sale price and I am waiting for the expansions to go on sale later. They would just be sitting unused while I played through the main game anyways.
There is no "main" game. Sins has absolutely no campaign/story mode. It's purely solo skirmishes or multiplayer.
That's not how the expansions work. They simply add functionality and features to the main game, making the whole thing (much) better. At no point would you not be playing the expansions if you have them installed.
I believe you can actually play without the expansions even if you have them installed. A time when you might want to do this is, for instance, if you wanted to play a match with other players who didn't have the expansion(s).
Or if someone has Entrenchment but not Diplomacy, you can just play without the Diplomacy expansion by running Entrenchment and then you can play together.