How can I loop through checked entity reference values with a taxonomy condition?
The first (crucial) part of your rule is a Rules Action to perform a Loop. If you're not familiar with such loops, then I strongly recommend to have a look at the tutorial titled "Lists and loops".

So add a loop related to the flavors that got selected. After you do, you should iterate over each item in that list (= each flavor).

And for each iteration you should then perform an appropriate verification if it is a premium flavor (in which case you want to add $5). But, within Rules Actions, you cannot just add another Rules Condition (as you may have noticed) ... Except if you use the Conditional Rules module (which is exactly the purpose of this module ...).

Done

PS: are those funds still available?