It is not just custom app created with bench new-app app_name, It also has setup like this How Add nodejs App to frappe & bench? - #7 by MartinHBramwell
What frappecloud cannot do (on 2025-03-03):
- Scale or auto-scale by adding more VMs (scale-out)
- Add custom backends and reverse proxy with frappe site
- use forked bench command or frappe framework