You seem to be conflating two grammatically different functions.
本 as a single word can be used directly in front of a noun to mean something along the line of "this X we're talking about," where X is the noun 本 precedes. I think this use is what you mean by a "general purpose prefix" that means "this."
The character 本 can also be part of a single word. If you look up many stand-alone words with 本 in them, you'll notice that there are certain patterns in meaning. If you analyze these words as systematic compounds, one of the hypothetical meanings the character 本 systematically contributes can be translated as "genuine," "true," "real," or something along those lines. (To be clear, the sense of "this" is also an example of various possible senses in some kanji compounds. The point is that there are two different things going on in OP's question; 本 can be a stand-alone word with the "this" sense but can also simply be part of a word, where the semantics can be sort of predicable due to the fact that words with 本 tends to have shared senses. The shared senses can be "genuine," "true," etc. or "this" or something else like "book".)
These two uses of 本 are different in that the former is simply a word that always precedes a noun due to its semantics while the latter is part of a single word that can't be divided any further. In fact, the former is a full-fledged single word 本 that has its own pitch accent, which is ほん{HL}. This pitch pattern does not change regardless of what noun follows it. But the latter does not have a defined pitch pattern in the sense that the whole combination gets its own pattern instead, e.g.,
本マグロ = ほんまぐろ{LHHLL} and
本わさび = ほんわさび{LHHLL}.
As you can tell from the fact that マグロ as a single word has a different pitch pattern (まぐろ{LHH}), 本X of this kind is a stand-alone, single word on its own.
Now, because the former usage is simply a word on its own, grammatically speaking, you can put pretty much any noun after it as long as it's semantically valid, although there are many words that just wouldn't appear after 本 of this use in normal context. But the latter use is valid only when it forms a legitimate noun when combined with the following word. Of course, you can coin a new noun by attaching 本 on the spot if you want. And if it makes sense and sounds great in the situation you are in, there's nothing wrong about it. Your new word may catch on among other Japanese speakers. Lots of words have been coined this way anyway. But you should note that there is a difference between the former use as a stand-alone word and the latter use as a "prefix" within a single word.
You can still say that they're both prefixes within a word or both stand-alone words, or even something different, depending on how you define "prefix," "word," and other grammatical terms. But there is a huge difference in versatility because the former behaves just like any other single word while 本X of the latter kind is valid only if it forms a real word or the whole "sounds legit" as a single word.
As for sound changes, the former does not introduce the h -> p/b change. The latter tends to cause this sound change.