The End Crystal should technically be on to of the obsidian not one block underneath as the bedrock base should be on top of the tower; for all you haters out there this is every tower!:

As I was trying to defeat the end, I noticed that on some of the towers the End Crystal was not there but there was still a beam going to the End Dragon, so I went to the top of the tower and the Crystal was one block underneath the obsidian:

Steps to Reproduce:
1. Enter the End
2. Go to every tower and see for yourself