I eat the cost of configuring it manually when I start up something new because it's just not that big of deal, even when you're like me, working across myriad languages and frameworks and organization with varying standards. It's not ideal, but it's not deal-breaker.
I do wish that there was a better way to definitively set it up a particular way and know that it is doing what you want it to do. I want something like presets/profiles. If I'm working with typescript, I want to be able to set it up to use a specific version of tsc, eslint, prettier; I also want to be able to create a different one with biome; I want it to work correctly whether I have my source in the project root or in a sub directory or in a monorepo tree.
Fairness to Zed: it is difficult to support all of these permutations, but I do think that they ought to be able to do something better to abstract these things and make the reusable.