Different Taiwan tax rates for husband and wife?

As far as I know, you (as a foreigner) cannot use the downloadable tax return software independently of your wife because the system will not recognize your ID number. Therefore, your wife is almost certainly filing a joint return for the both of you, with her listed as primary taxpayer and you as “the spouse”.

Filing your taxes in this way means you have relinquished your rights to obtain information and certification to the primary taxpayer for the relevant years IN PERPETUITY. See my post here, for how that gave me a ridiculous amount of trouble: A warning for foreigners filing joint taxes

I’m sorry that doesn’t really answer your question, but I would be very surprised if the program is truly calculating independent taxes based on my own experiences.