Following up… It looks like if you change the defaultOptions in vendor/assets/javascripts/markdown-it.js so that fuzzyLink is false, as Sam suggested, it solves my problem. But doing so creates a big headache because we don’t want to manually redo that change every time we update.
Then I stumbled on a simpler solution. The markdown linkify tlds setting is a list of top level domains that are assumed to be URLs by fuzzy linking. If you remove all those TLDs and add just one fake TLD that would never actually show up in a post then it effectively disables fuzzyLink. You need at least one TLD in the list or apparently anything that ends with a . will be treated as a link.
So no need for a code change, we can disable fuzzyLink my removing the real TLDs from the setting and adding a fake one.