1) Create any world in creative mode with default settings (cheats, structures,...)
2) Get an eye of ender in your inventory to look for the End Access room of a stronghold
3) Once there, dig down to search for the room
4) Picture #1 shows how I see the end portal, the stone brick are real and are mined as normally (don't pass trough or stuck inside)
5) Reload the world by exiting and reloading
6) Picture #2 shows : all the stone bricks are gone and show the normal stronghold access

It seems like all the air and misc blocks of the chunk are replaced by stone blocs under the surface. By digging further I can reach lava which is located at the entrance of the room.
While testing on several worlds, I arrived at a point where the end portal room was under a jungle biome. While at mid-air trying to dig I was stuck by something invisible an untouchable. After reloading, tree leaves appeared where I was stuck.