The sentence, "The grocery store has standard butter, but it will soon be substituted for organic butter" makes no sense to me. Since "grocery store" is the subject of the first clause, I first assumed "it" referred to the store and wondered how a store could be substituted for butter. It's not clear what "it" refers to in this sentence.
It's also passive voice: "be substituted" which does not indicate who is doing the substituting. So it's vague that way.
The word "substitute" can be used as a verb, "to-substitute" or a noun, "the-substitute". The first implies that you are switching the original for something else. The second implies a surrogate or stand-in, which is the opposite. But I think the sentence is clear in this regard because standard butter will be substituted for organic, meaning standard will win. If it said, standard butter will be substituted with organic, then organic will win, although in American English, that sounds very awkward to my ear.
Please don't take this personally, but your first sentence is really poor for all the above reasons. I think, "The grocery store will soon substitute standard butter for organic butter" is a much clearer sentence.