The base currency you set here is used throughout Koinly. It can only be set to a fiat currency. However, this does not mean that you are not allowed to purchase crypto using a different fiat. You can transact with whichever currency you like but the market prices, cost basis and capital gains/losses will all be calculated in your base currency.
It is recommended to set it to the currency you will be reporting your taxes in or the currency you use to buy most of your cryptocurrencies.
Koinly supports all major fiat currencies.
Note: This list only shows the first 25 results, you will need to type in the name of your currency if you can't find it in the list.