You're going to see things that they're doing that you think are stupid, with no possible justification. Don't say anything... yet. Give it time for you to learn whether or not there actually are decent reasons for what they're doing.
I agree that saying "that's stupid" is stupid. But asking "why do we do it this way" or "have we looked at npm recently" or "why does this return a 403" could actually start a discussion and be constructive on both sides.
I wouldn't hire someone who swallowed their opinions until they were sure they couldn't be wrong. I'd much rather hire someone who is willing to ask questions and suggest alternatives. I don't care if three people that same day have done the same thing (and that alone is likely a signal that I've made a weird call somewhere).
I'm saying don't say those things right away. I'm saying don't walk in there saying "this is all stupid, you should do everything this other way, how come you all are so dumb" on the first week.
(Remember, this is "advice for the first 90 days", not "advice for the duration of your employment there".)