Bun preset doesn't work for TanStack Start `createFileRoute` $ API endpoints

Environment

Dynamic API endpoints created using createFileRoute in TanStack Start are not being registered when using the Bun preset. All API route requests return 404 errors instead of executing the defined handlers.

Reproduction

1. Make a $ route:

example:

import { createFileRoute } from '@tanstack/react-router'
import { reactStartHandler } from '@convex-dev/better-auth/react-start'

export const Route = createFileRoute('/api/auth/$')({
  server: {
    handlers: {
      GET: ({ request }) => {
        return reactStartHandler(request)
      },
      POST: ({ request }) => {
        return reactStartHandler(request)
      },
    },
  },
})

2. Build using preset:

plugins.push(nitro({ preset: 'bun' }))

Describe the bug

All API route requests return 404 errors instead of executing the defined handlers.

Additional context

"nitro": "3.0.1-alpha.1",

bun --version
1.3.2

Logs

none

Start with the reproduced createFileRoute('/api/auth/$') example and the Nitro configuration using preset: 'bun'. Build the application with Nitro 3.0.1-alpha.1 and Bun 1.3.2, then inspect why requests to the dynamic API endpoint return 404 instead of invoking the declared GET and POST handlers. Done means those handlers are registered and API requests no longer return 404.