The OEM front pads are a composite ceramic material - should be pretty quiet compared to anything you can get aftermarket. Organic would definitely be "softer" - but you'd loose some high temperature stability and overall dusting resistance.
That said, I'm surprised that you found the drums to be out of round. Drums are pretty tough to distort like that, takes a very specific set of conditions to do that. Did they happen to mention by how much they were egg'd out? Even if you drove a lengthy highway commute with the parking brake engaged - unless the rear end was immediately quenched in ice cold water at the end, they will still be perfectly round.
Turning down rotors are the same way - did they mention how much run out they measured? Factory specs do allow for some surface refinishing, removing the tiniest bit of material to allow a new pad to properly transfer some of its material to the rotor face, to ensure a even transfer layer for proper braking action.
With pretty much any rotor out there, if it is warped enough that it has to be turned down to get back into spec - you are way further ahead if you just outright replace them. The different between a brand new rotor and one that is too thin is on the order of a couple of mm of material. Depending on how badly "warped " the rotor is, they can easily get that rotor too thin (still outside the minimum thickness, but now much easier to warp again - especially if they don't get the surface finish correct).
On my 8th gen, even with the typical treatment, eg. rotor scored, turn down 0.060" - then fast cut at 0.002"-0.008" to get the correct RA - if I did that to a brand new rotor, I've just shortened it life by half.
Assuming they put on new OEM pads - there really isn't a big procedure to bed those in - just drive normally, avoiding abrupt and lengthy high-speed stops. Those pads are already pre-sintered, so they bed in almost immediately.
But much of this is also dependent on the rotor face finish. If the shop didn't get the right surface finish - usually referred to as roughness average (RA) - in the approved range (usually between 40 to 80 microinches) - then the pad bedding process can be disrupted. For RA, lower numbers usually preferable - I personally shoot for 50-60 with a ceramic or organic pad, lower for a more aggressive one - but anything lower than 20-30 - basically just grinding material, no need to go that rough. Problem is - you cannot visually tell the difference between 40 or 80.
I have to assume that they used the OEM pads and installed the pads correctly. That leaves just the work they did on the rotor. If the finish RA is off or if they didn't cut enough material or removed too much material - you'll get weird braking behavior - like excessive noise, squealing, hard braking, inconsistent braking, pulling, etc.