The pathPrefix url filter isn’t needed here for permalinks. Otherewise the files generate to a special folder. We want the directory output to look the same, not with hardcoded pathprefix directories.

feed/feed.njk

@@ -1,6 +1,6 @@
 ---
 # Metadata comes from _data/metadata.json
-permalink: "{{ metadata.feed.path | url }}"
+permalink: "{{ metadata.feed.path }}"
 eleventyExcludeFromCollections: true
 ---
 <?xml version="1.0" encoding="utf-8"?>

feed/json.njk

@@ -1,6 +1,6 @@
 ---
 # Metadata comes from _data/metadata.json
-permalink: "{{ metadata.jsonfeed.path | url }}"
+permalink: "{{ metadata.jsonfeed.path }}"
 eleventyExcludeFromCollections: true
 ---
 {