...So my question is really... When making a short trade through Binance Margin, am I putting my Spot account at risk or just the money in my Margin account?
No, you risk only the amount that you transferred from the spot wallet to a pair with an isolated margin. If you use a cross margin account, then your losses will also be limited to the amount that you transferred to this account. The difference between isolated and cross is that in order to trade on an isolated account, you need to create liquidity for each pair separately, and on a cross account, you can open transactions on several coins.