Should spouses filing together, who both have traded bitcoin, mix transactions when calculating FIFO cost basis?

There are several considerations here. I'm going to assume that bitcoin brokers report trades to the IRS in the same manner as traditional brokerage firms do. If they do not, the IRS requires that you report all bitcoin transactions.

In the U.S., the IRS considers bitcoins as assets, rather than currency so long and short term capital gain holding periods apply (one year).

If your broker does not already do it for you, you should pair off buy/sell trades made in each account. You should not pair a trade made in one account with that made in another account unless you have either combined accounts or you have taken possession of the asset. You will then list the gains and losses from each account on your tax return.

All of this is much ado about nothing if you are using FIFO. If you were using lot designation (again assuming the same allowability as traditional brokerage) more for beneficial tax treatment then it would be more complicated. But I think that's a different story since you have asked about FIFO.