Yes, Latin centum means 100; hence century, and the prefix centi was invented during the French Revolution, meaning 1/100 (https://en.wikipedia.org/wiki/Centi-). For hecto-, they took inspiration from the free ἑκατόν (https://en.wikipedia.org/wiki/Hecto-)

(They did the same for 1000 and 1/1000, deriving milli from Latin millum and kilo from Greek χίλιοι, but used Latin for both deca- and deci-, and used Greek for both giga- and micro. So far for consistency)

I don’t see how it follows that either usage is acceptable.

That’s like saying risky and riskless can be used interchangeably because the both come from the word risk.

Edit: I don’t know why I even reached for an analogy, it’s exactly like saying hundred and hundredth are interchangeable.

No it's like saying biannual can mean twice a year or once every two years.

Dictionaries are descriptive, not prescriptive. Language evolves.

Maybe, but in Europe, you'll finish off your 33 or 50 centilitre beer in a sitting and possibly a few more.