Negative amounts are correct, if you have open margin positions.

Lets imagine you have $100 USD. And you buy 0.3 btc for 300USD using Bitfinex x3 ledger

What do you have after that trade? If we say that you only have 0.3 BTC, that would be very wrong because that means you don't have the 200 USD debt that you must return after closing position - and your totals will look like you got 200USD out of nowhere. To fix that, we must record that you have both 0.3BTC and -200 USD and so in total you still have $100 just like in the beginning.