No, that's not the case. If you create any of those new objects, you have to explicitly add it to what you want it to be associated with. New fields have to be added to screens and schemes, new issue types associated with issue type schemes and then to projects, and so forth. None of this happens automatically from the admin side.
If you want to share stuff across projects, you can, but it is in no way a requirement.
> As a developer, this is a giant leap backwards.
The only Jiras I've ever seen suck that hard is when the end users are treated as hostile rather than stakeholders in the deployment. It can be as easy to use or as complicated to use as the people writing your workflows and screens.
That applies to the UI as well. The basic UI, OOTB, is fairly easy to understand. Once you have management dictating 30 different required fields along 50 different projects, each with their own issue types and workflows... yeah, it can get hairy.
> To see your PRs attached to a card, you have to click into the card, then click into the PR list.
This is going to be a bit "you're holding it wrong", but why would you expect to see PRs at the card level rather than the detail view? The agile board is meant to show who and what, not how. PRs would be meaningless noise to the average user of an agile board, not to mention taking up the limited space available on a single card.
Those issues aside, you'll never hear me accuse Jira of being easy to administer. It's a tool that tries to be all things to all people, meaning it will take a non-trivial amount of time to get your head around and have some rough edges.