TS6059 error while building project in monorepo setting #1709

Problem

I have a browser extension project which depends on various packages within monorepo.
After updating to typescript 6 it doesn't build anymore due to resulting in errors like this:

ERROR in {package_module_path}
link-overwatch:build: [tsl] ERROR in {module_path}
link-overwatch:build:       TS6059: File {module_path} is not under 'rootDir' {extension_project_path}/src'. 'rootDir' is expected to contain all source files.
link-overwatch:build:   The file is in the program because:
link-overwatch:build:     Imported via {another_module_path} from file {module_path}
link-overwatch:build:     Root file specified for compilation

However it only triggers like this when building, during development it works just fine.

Reproduction

Install project

git clone https://github.com/GabenGar/todos
cd todos
# have to invoke prune with `npx` because it's called prior deps installation
# https://turborepo.dev/docs/reference/prune
npx turbo prune link-overwatch
cd out
npm ci

Run npm run dev-extension to start development mode, which will open a new firefox profile instance (so firefox is required). Possibly restart several times, since I haven't found the solution for starting web-ext in parallel but only after webpack produces output. But the point is it will work just fine and build on webpack side without path resolution errors.
Now run npm run build-extension and get bombarded with errors.
It couldn't be due webpack misconfiguration, because ts-loader gets used in both environments. There is also nothing inherently wrong with @repo/ui workspace structure, since its code is consumed by two other frontend projects, one isn't even using webpack. Nor I don't see any anomalies in tsconfig.json. So I assume the problem is ts-loader behaviour specifically with typescript 6+.