I'm particularly fussy about the new laptops I put into service each year.
Because of that and having the same question (a few years ago) about Time Machine as the OP has posted, I've run side by side tests. One using Time Machine to setup my new MBPr and One test doing a conventional "clean install". The end result is identical. This was proof positive for me that Apple's engineering team did a fabulous job with Time Machine.
I enjoy using Time Machine for it's speed, convenience and excellent results.