Well, this allows the extension to at least show up and "work":

pkgs.gnomeExtensions.custom-reboot.overrideAttrs (old: {
  postInstall = ''
    ${old.postInstall or ""}
    sed -i 's/43/44/' $out/share/gnome-shell/extensions/customreboot@nova1545/metadata.json
  '';
})

But it doesn't actually do what it's supposed to do. The menu of boot options it can show me is empty and I don't see any messages in journalctl

diff --git a/systemdBoot.js b/systemdBoot.js
index 22c2054..9599b0f 100644
--- a/systemdBoot.js
+++ b/systemdBoot.js
@@ -49,7 +49,7 @@ async function getBootOptions() {
         Utils._log(`bootctl list: ${status}\n${stdout}\n${stderr}`);
         let lines = String(stdout).split('\n');
         let titleRx = /(?<=title:\s+).+/;
-        let idRx = /(?<=id:\s+).+/;
+	let idRx = /(?<=id:\s+)(?<!machine-id:\s+).+/;
         let defaultRx = /\(default\)/;
         let titles = [];
         let ids = []
@@ -99,7 +99,7 @@ async function getBootOptions() {
 async function setBootOption(id) {
     try {
         let [status, stdout, stderr] = await Utils.execCommand(
-            ['/usr/bin/pkexec', '/usr/sbin/bootctl', 'set-oneshot', id],
+            ['/run/wrappers/bin/pkexec', '/run/current-system/sw/bin/bootctl', 'set-oneshot', id],
         );
         if (status !== 0)
             throw new String(`Failed to set boot option to ${id}:\nExitCode: ${status}\nstdout: ${stdout}\nstderr: ${stderr}`);
@@ -109,4 +109,4 @@ async function setBootOption(id) {
         Utils._logWarning(e);
         return false;
     }
-}
\ No newline at end of file
+}
diff --git a/utils.js b/utils.js
index d39baec..7d44513 100644
--- a/utils.js
+++ b/utils.js
@@ -48,7 +48,7 @@ const BootLoaderClass = {
  * Returns the path of the bootctl binary or an empty string if not found
  */
 function getBootctlPath() {
-    let paths = ["/usr/sbin/bootctl", "/usr/bin/bootctl"];
+    let paths = ["/run/current-system/sw/bin/bootctl"];
 
     let file;
 
@@ -191,4 +191,4 @@ function _log(msg) {
 function _logWarning(msg) {
     if(DEBUG)
         log(`CustomReboot WARN: ${msg}`);
-}
\ No newline at end of file
+}

Here's the patches I used. If anyone knows how to make the menu scroll, maybe I'll use it :P