"Names are parts of language, and the way language functions is governed by rules and natural laws of phonetics. People who say, "Well all names started somewhere" are correct, but if you go back to ancient languages (Greek, Sanskrit, Akkadian, etc), you find that most names are comprised from meaningful phonemes that recur throughout the language. So there was no random flinging together of sounds at any point. This meant that there was a time when most people were wandering around with names that literally meant things like "victory of the people" (Nicodemus) in the language that the person wearing the name spoke. There were linguistic conventions about how words were combined into a name, and that is how the spellings were determined. So there's one factor.
Then there is the fact that people speaking different languages with different phonetic inventories were in frequent contact. The result is that you might have a speaker of a language that has a v sound in contact with someone whose language has a b sound. Phonetically, those two sounds are extremely similar, and so a name like Basileios (Greek) might get adopted as Vasilii by speakers of Slavic languages (to name just one example). In a period of extremely limited literacy, this is how spelling and sound changes occurred and how legitimate variation in the spelling of names came to be. Also, languages have rules about how words have to end, how verbs have to be conjugated, etc, so a foreign word would be remolded to fit into the phonetic and morphological parameters of a given language.
The important thing to understand about this process is that none of it was arbitrary or anyone deciding, "I like the way this sounds/looks better." There was no individual creativity involved. Another important thing to realize is that we no longer have the excuse of being a primarily oral culture with very low rates of literacy. Also, as speakers of English, we have a massive phonetic inventory because English is such a mutt of a language. So there are really relatively few names of Indo-European derivation that we don't have the right sounds to be able to say. Random stylistic choices of individuals are not legitimate reasons to change the spelling of a word as long as it is phonetically comprehensible in the language you speak.
For example, Jackson is extremely straightforward to pronounce in English and has a meaning (son of Jack). Replacing the cks with an x is completely phonetically unnecessary for pronunciation purposes and is therefore just a misspelling. It would be like someone deciding they prefer the way sed looks to said and proceeding to misspell the word in all subsequent formal and informal written communications. This decision would make that individual look like they were poorly educated and/or didn't understand the concept of spelling. The same principle applies to names. If someone were to say, "I want to name my child Sharlot," I would assume that they meant Charlotte but found the spelling to be unintuitive or too common. In the former case, this would clearly indicate a lack of quality education. In the latter case, they would be making a change to the language based on a desire to be different, which is not how the rules of language evolution work.
So that is why it matters to us how a word is spelled and not just whether we could sound it out and end up with something that sounded like a real name."