And they'd sure love to be in charge of our code repo.
Mh - i'm not a native speaker. I didn't understand this line.
Tom was saying that the JIRA/Atlassian people would happily volunteer to host our code repository for no cost (in money) to us. The implication being that they have their own interests for doing so. The obvious reason is the free advertising, but the reader might infer less altruistic motivations, which Tom referenced with his next sentence
And the main, possibly only, metadata they can track about an issue is
"assignee" and "milestone".
Having spent a large portion of my life in the Midwest US and Texas, I'm painfully aware of how often native English speakers speak in idioms and hyperbole.
(example: "painfully aware" - I am not in actual pain, I'm mildly embarrassed. I'm also not that "aware", as I managed to use hyperbole in my sentence lamenting the use of it.)