I'm coming in brand new to this world, so I have no bias towards the old or new way.
I will say however, that I thought it was really weird to do the criminal background check component as part of the medical exam.
I have an old misdemeanor that I'm having to put on there and explain to the doctor who is doing my physical?
I don't know what the new TSA rules are, but it seems more logical to have the medical part being about the medical stuff and having <insert government agency of choice> doing the background check portion.
That being said, bad guys don't follow the laws/rules anyways so I doubt the old way or new way is going to do anything to curb an intentional criminal/terrorist act.