According to the LSP logs, the root directory is always that of the current working directory when the LSP was added:
In /path/to/lua-language-server/log/ a log file for this working directory shows up containing

  rootPath = "/home/konfekt",
  rootUri = "file:///home/konfekt/",

after Vim was started in ~/, editing a file in a project dir below ~/, throwing an error that more than 100000 files were scanned.

Instead, one would expect the rootPath to be set to the current working directory.

According to https://luals.github.io/wiki/faq/#why-is-the-server-scanning-the-wrong-folder

When not using Visual Studio Code, check the rootUri field in your configuration - some clients allow users to customize this value. If the value is correct or cannot be modified, please report the issue to the developer of the client you are using.

I am using latest LSP master and Vim 9.1.369 on Ubuntu 22.04