Apple doesn't sign them. A free developer account allows you to sign your own apps with a 100 device limit (per employee, if you work at a small company, or unlimited if you pay extra as an "enterprise" developer - which doesn't actually require being a large enterprise. It basically just costs extra).

They only need to sign the app if you want a large team of external beta testers - then you have to send the binary to Apple to be scanned for malware and signed by them.