The reason was that the keyed in bootloader didn't have the instructions to detect the end of tape signal (because that would have required more instructions to be entered with the switches). The short piece of tape with the "real" loader just kept going. In normal operation, when EOT was detected, the reader stopped and the trailer was enough to keep the tape from flying out.
I used machines where the inhibit line of the highest words of the core memory was wired to a switch to disallow overwriting the loader once it was read in from the tape. It limited usable memory by 128 16-bit words as I recall, which was over 1% of the 8k words, but the trade-off was almost always worthwhile. And if you really needed that memory, you got to shoot the bootloader tape across the room when you were done!