fix(config): read workspaceRoot only form CLI options

.changeset/hip-pugs-smell.md

@@ -0,0 +1,5 @@
+---
+"@pnpm/config": patch
+---
+
+workspaceRoot should only be read for CLI options.

packages/config/src/index.ts

@@ -217,6 +217,7 @@ export default async (
   ]) as unknown as ConfigWithDeprecatedSettings
   const cwd = (cliOptions.dir && path.resolve(cliOptions.dir)) ?? npmConfig.localPrefix
   pnpmConfig.workspaceDir = opts.workspaceDir
+  pnpmConfig.workspaceRoot = cliOptions.workspaceRoot as boolean // This is needed to prevent pnpm reading workspaceRoot from env variables
   pnpmConfig.rawLocalConfig = Object.assign.apply(Object, [
     {},
     ...npmConfig.list.slice(3, pnpmConfig.workspaceDir && pnpmConfig.workspaceDir !== cwd ? 5 : 4).reverse(),