Seems to me the Capital+Crypt deck, in reality, will be a little messier to set up than I described. I was just reducing it to the bare minimum apples-with-apples comparison to highlight the pretty substantial deck-thinning effect of leaving so many cards on the table between turns.
The reality is that you'll probably have one or two Silvers or $2 action or whatever for early economy as you're trashing. Even if you buy Capital first, a single Capital/Silver/Silver turn buys two Crypts and then you're in business, paying off the debt quickly and buying engine parts two at a time. If you buy Crypt/Capital first, a Capital/Silver/Silver/Crypt lets you get another Crypt/Capital with no debt, and every pair you buy adds two cards that won't increase your deck size because they're staying on the table every turn, eliminating the need to buy more draw along with it. By comparison, every time you buy Gold, you have to buy more actions/draw to get it in hand, slowing down the Gold version by comparison.