I love Zed, but I hear you. It's a very fast and capable editor with lots of IDE features, but it's lacking comfortable ways of tuning it for specific projects. (This is a problem with every general purpose, everything-to-everyone kind of IDE versus stack "native" IDEs that are geared toward the one true way of developing for particular target.) The configuration file structure is arcane, and it certainly not clear what the boundaries are between language feature configuration, LSPs, built-in and third-party code quality tools, etc.
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.