They do produce the same thing but not in the same way. Their relevance is the same as having more than one way to generate gold in the first place I would argue
First of all omens are active for a duration so your assessment would not necessarily be what would make you more money immediately.
Second the situation may be more complex than you think. Here’s a few things to complicate it:
1: Commerce comes from trade. It is dependent on you having a high number of trade routes open over time (preferably foreign trade routes), these might be broken by war declarations, annexations, etc.
It is further modified on a local level by your citizens. Choosing this omen means to some extent you expect citizens to keep being happy (and therefore productive). Are your citizens in the trading provinces of your own culture? If not they’ll be affected by AE.
2: Tax comes only from slave and tribesmen pops. It’s therefore dependent on these pops remaining happy over time for being efficient. It would also suffer greatly from hostile sieges stealing your pops or unhappiness.
Are your tax producing pops of your own culture? If so they’ll be mostly unaffected by AE, if not then conquering new lands will lower the tax and make this omen less worthwhile to take.
You can have many other things affecting these, both temporary and permanent. For some countries commerce might always be the better choice. But it’s not necessarily always an easy choice, and it may turn out the other one would’ve been better in retrospect