Just checking that the "make a run" effects on Account Siphon Doppelganger doesn't cost a click to perform like in a regular run (aside from playing the cards, or satisfying the conditions of the card).

Not entirely sure what you're asking. If you have Doppelganger in play and play an account siphon event (costing a click) which ends up as a successful run, you could then choose to make another run (free from the console, does not cost a click) anywhere you choose. The 2nd run would not be an account siphon, nor could you play any other event: run cards, use sneakdoor beta, etc. Hope that helps.

Nope. Making a run is an effect. The rulebook action is just one way of making a run.