(There's a separate issue here where a system for a specific pair of languages might get codified and become "frozen in time" even as either or both languages evolve. For example, the Russian Polivanov system for transliterating Japanese uses "си" for "シ" because the standard pronunciation of "щ" at the time was more like "шч", similar to Ukrainian, so it was clearly the wrong choice back then - and yet clearly the right choice now if not for backwards compatibility concerns.)
OTOH Polivanov seemingly tried to reflect actual pronunciation, thus ツ is "цу" (tsu), ふ is "фу" (fu), を is "о", は is "ва" (va) when it's a particle, the syllabic nasal is "m" in environments where it is so pronounced etc.
The only real mystery about Polivanov system from this perspective is why ち is "ти" (ti) and not "чи" (chi).