Flight to Taipei is very likely on Eva. I am not sure if we can use OP miles to upgrade on Eva. If not, then there is not difference between the booking class. Personally, I would book the flights directly with Eva and book the Evergreen Delux cabin. It is always MUCH cheaper than booking on CO.com. Of course, you run the risk of getting 50% EQM for the domestic segments.

I hope Eva stays with Continental when it moves to * Alliance.