In theory, yes - you can set different settlements for each currency that you accept. However, in some cases, you might have to create a separate merchant tool. For example, there is no possibility to split Bitcoin earnings using one merchant tool. In this case, you would have to create a separate payment button / PoS / API for different payout options in order to receive both fiat and Bitcoin. This, however, is not possible for e-commerce plugins.
Learn more about changing invoice settings here.
Learn more about payout and settlement options here.