UPDATE
This was the response from the store after they got a call from Trek (I called Trek to complain)
"We switched both front and rear pads.
We go through the bedding process here. You are going to get a little noise from the brakes under hard stopping. That is normal.
I spoke with SRAM this morning. I went through and confirmed all braking components are tight and torqued to spec. SRAM recommended resurfacing and cleaning the rotors again and to check for any signs of contamination. There are no signs of contamination, everything is torqued to spec, clean and aligned. I don't think this is a Trek issue."
The brakes are indeed making less noice, but not as bad. However, as said here, they seem to be cutting corners and not dedicating the time they should or replace parts.
I picked up the bike today and dropped it at another store (same company). I spoke with the tech manager and they will work on it.