Centurions were soldiers. Prefects were not. The prefectship was a minor, non-elected magistracy. Prefects were selected for their office by elected magistrates to stand in for them in certain duties--in other words, they were a part of a magistrate's personal staff, though they did not have the dignitas that came with election to, say, the quaestorship. As such they were in a completely separate class from centurions, who were still members of the soldiery. In the case of camp prefects there can be no question of equal rank with a centurion, though the most senior centurions held high status. The camp prefect as an office was established by Augustus as part of his program to establish a truly standing army unaffected by the regular rotations of provincial magistrates as in the Republic. Camp prefects were appointed directly by the emperor and under Septimius Severus was renamed the legionary prefect (praefextus legionis). By the end of the Principate the legion are prefect was the commanding officer of a legion, not legates. Generally speaking the camp prefect was considered a promotion from the centurionate, and the senior centurion of a legion was usually elevated to equestrian rank and promoted either to the prefectship or to the military tribunate

Praefectus Castrorum is a position that the legion's most senior Centurion, the Primus Pilus, can be promoted to. The Primus Pilus (first file/first spear) commanded the first century(a double century) of the first cohort of the legion. The Praefectus Castrorum was not a simple quartermaster, but was in charge of many aspects of the legion; training, logistics, and organization. In a modern battalion, he would have similar duties to an executive officer, although he was not second-in-command. So to answer your question, yes the Praefectus Castrorum outranked a Centurion.

Here's a simplified rank structure of a Legion:

Legatus Legionis

Tribunus Laticlavus

Tribuni Angusticlavii (five members)

Praefectus Castrorum

Primus Pilus (Senior Centurion)

Primi Ordines (First Cohort Centurions)

Centurion

Optio

Decanus

Legionary