Profit/Loss (P/L) in margin trading on Bitfinex is always settled in the last symbol of a pair.
If you open a long, you buy BTC using margin funding (USD), if the price rises you sell the BTC and realized P/L, which equals [amount] * ( [sell price] - [buy price]) , will be for you to keep, which will be USD (or to pay if you realized a loss).
If you open a short, you sell BTC (your own BTC + margin funding BTC) and when the price drops, you buy them back to close the position. [Amount] * ( [buy price] - [sell price]) will be for you to keep, which will be in USD (or to pay if you realized a loss). This is again in USD, as you will have a bit of USD to spare in order to buy back the BTC previously sold at a higher price.
If you only want to hold BTC after closing a margin trade, you will need to manually exchange USD profits into BTC using the BTC/USD pair by highlighting "Exchange" in the Order Form box on the trading page.