Yes they are cut-out on new ones.
A little at the back can't hurt if needed to level it up for lock-up if it doesn't make it too tight, you might just slip some aluminum shims under it first to see before going that route in the back.
If it gets too thick down in there, it is a little more difficult to get out. I good sharp wood chisel with the bevel down and the right width will make short work of it though. Be careful if you use a chisel though....there are more carpenters and individuals injured every year from using a wood chisel than any other tool !!! Some study said combined tools don't have as many as chisels...I think it is because they are so razor sharp and most folks don't know the proper use.....you are right, the proper use is not JB weld......but it works