Most of the time when people make a brachah on besamim during havdalah they are using one species of spice. If that is the case, then the proper brachah which should be made is בּורא עצי בשׂמים if it's attached to soil, בּורא עשׂבי בשׂמים if it's an herb/grass/flower NOT attached to the soil, or הנותן ריח טוב בּפּירות if it is an edible fruit. בּורא מיני בשׂמים is only for where there are multiple species of spice. If one is only using one species, should they change the commonly made brachah or should they try to use multiple species or something else?
Mishnah Berurah 297 Seif kattan 1 says the minhag is always to say borei minei besamim at Havdalah, regardless of what you're using for spices. He writes the reason is to avoid people making a mistake in which bracha to make.
However, he advises to use a spice who's bracha is usually borei minei besamim. He doesn't say multiple spices as you suggested, but rather a single spice such as cloves. Your assertion that borei minei besamim is only for multiple spices is incorrect. It's like the "shehakol" of scent brachos. SA 216:10 says if you have multiple spices you usually make the bracha appropriate for each one (like you would when eating fruits and vegetables), while the Rema adds borei minei besamim would cover them all, that's not lechatchila. SA 216:2 says borei minei besamim is lechatchila when the spice is neither from a tree nor from plants, and gives the example of musk.