Hi,

One of my players confirmed both creatures can still somehow break the blocks. I'm not sure how.

Using:
[1.12.2]+SecurityCraft+v1.8.10
forge-1.12.2-14.23.5.2768-universal

Maybe some other mod?
Has this been tested by a non-creative player in a room that spans multiple chunks?

I'm not sure why the updated didn't fix it for my server.

Already fixed for the Wither, the Ender Dragon won't be supported. The fix will be out in the next version.