Scaffold .editorconfig and patch it instead of disabling it.

composer.json

@@ -290,7 +290,6 @@
         "web-root": "web/"
       },
       "file-mapping": {
-        "[project-root]/.editorconfig": false,
         "[project-root]/.gitattributes": {
           "append": "drupal_scaffold/gitattributes_append"
         },
@@ -318,5 +317,10 @@
       "web/modules/custom/{$name}": ["type:drupal-custom-module"],
       "web/themes/custom/{$name}": ["type:drupal-custom-theme"]
     }
+  },
+  "scripts": {
+    "post-drupal-scaffold-cmd": [
+      "patch -p1 <drupal_scaffold/editorconfig.patch"
+    ]
   }
 }

drupal_scaffold/editorconfig.patch

@@ -0,0 +1,15 @@
+diff --git a/.editorconfig b/.editorconfig
+index 686c443cec..ffd179a154 100644
+--- a/.editorconfig
++++ b/.editorconfig
+@@ -13,5 +13,9 @@ charset = utf-8
+ trim_trailing_whitespace = true
+ insert_final_newline = true
+
+-[composer.{json,lock}]
++# Note that this has been patched via Drupal scaffold from 4 spaces to 2 spaces.
++[composer.json]
++indent_size = 2
++
++[composer.lock]
+ indent_size = 4