Added E2E testing for spacing

This adds E2E testing for spacing and provides more appropriate comments for the changes made to `index.js`

cypress/integration/rendering/flowchart-v2.spec.js

@@ -760,6 +760,28 @@ A ~~~ B
     );
   });
 
+  it('3258: Should render subgraphs with main graph nodeSpacing and rankSpacing', () => {
+    imgSnapshotTest(
+      `---
+      title: Subgraph nodeSpacing and rankSpacing example
+      ---
+      flowchart LR
+        X --> Y
+        subgraph X
+          direction LR
+          A
+          C
+        end
+        subgraph Y
+          direction LR
+          B
+          D
+        end
+      `,
+      { flowchart: { nodeSpacing: 1, rankSpacing: 1 } }
+    );
+  });
+
   describe('Markdown strings flowchart (#4220)', () => {
     describe('html labels', () => {
       it('With styling and classes', () => {

packages/mermaid/src/dagre-wrapper/index.js

@@ -54,8 +54,8 @@ const recursiveRender = async (_elem, graph, diagramType, id, parentCluster, sit
       if (node && node.clusterNode) {
         // const children = graph.children(v);
         log.info('Cluster identified', v, node.width, graph.node(v));
-        // node.graph.setGraph applies the graph configurations such as nodeSpacing to subgraphs as without this the default values would be used
+        // `node.graph.setGraph` applies the graph configurations such as nodeSpacing to subgraphs as without this the default values would be used
-        // We override the `rankdir` variable to allow for the subgraph's direction to override the graphs direction in the subgraph
+        // We override only the `ranksep` and `nodesep` configurations to allow for setting subgraph spacing while avoiding overriding other properties
         const { ranksep, nodesep } = graph.graph();
         node.graph.setGraph({
           ...node.graph.graph(),