@asashdor gave a very good answer to the general situations presented – without any more specific information about a particular player’s case, he is absolutely correct.
It is better to go to specifics than to try arguing from generalizations, particularly when the generalizations don’t match up very well (i.e. comparing a case with two on-use trinkets to a case with azerite gear, like what happened here). So let’s get some actual setups here and see what’s going on for real:
@feaver If you would like to give me a specific case where you think the optimizer is recommending two on-use trinkets when you have another alternative that would be better, we are more than happy to look at it in detail. Post your export string that you copy from the in-game addon to the website, and we can reproduce your case.
The optimizer does have corrections for using two on-use trinkets together: it does tend to reduce the value a bit, though sometimes not enough to make one of your other trinkets better. When you post your case, we can take a look and see what’s up – maybe one of the corrections needs adjusting, or maybe it just is what it is and you should give it a try.
@tkalfaoglu if you want to do the same thing: post the export string that you copy from the in-game addon to the website, we can look at your specific case and see why it would recommend a lower item level azerite trait in your specific case. Most likely, your higher ilvl item has a weak trait and/or your lower ilvl item has a strong trait.