As a new hire there is a line to walk between on one hand, using your outside/fresh perspective to provide valuable insight to the org, and on the other, complaining (or appearing to complain) about decisions where you don’t have full context.
Many of the examples in the OP are probably closer to the former, but my general advice here is to keep lots of notes about what seems broken, and revisit in a month or two. Sometimes you gained context that explains why something is actually sensible. If it still seems crazy with context, you can now bubble up the feedback with confidence, and also having hopefully built some respect and trust from the team to make the message land better.
Many of the examples in the OP are probably closer to the former, but my general advice here is to keep lots of notes about what seems broken, and revisit in a month or two. Sometimes you gained context that explains why something is actually sensible. If it still seems crazy with context, you can now bubble up the feedback with confidence, and also having hopefully built some respect and trust from the team to make the message land better.