@.access:
They don't look similar, they are the same. フ, ブ and プ are the same syllable. The diacritics are included in the last two cases for phonetic purposes, but they are the same. Think of them roughly as accents: "a, á, ã" are all the same letter (a).
Well, my mistake then. Even though they're the same letter, there's still a phonetic difference like you said.
And yes, that's the whole point, unless you believe Oda is so worried about not repeating the same letter for two SH in latin alphabet but not about doing the same in his own alphabet (the one the manga is actually written in).
Who's to say he wasn't? Maybe he just liked the sound and spelling of "FRANKY" and "BROOK" and didn't mind that the first character of their names in kanji were the same. The diacritics making them sound phonetically different when spoken aloud might have helped, too.
That's just my theory.
And despite recent romanizations (Levely), I'm confident that Oda at least recognizes the differences in the latin alphabet for the names of his crew. He has written "LUFFY, ZORO, NAMI, etc." thousands of times by now.