I am also a bit surprised that they are insisting on 16 bit files. That seems a bit odd to me. If you have done all the recording and mixing in 24 bit then the best way is to master is do all the mastering in 24 bit as well and dither down to 16 bit usually in the limiter (eg ala PSP Xenon. I also see that PSP have released a special dither plugin which also looks very interesting.)
So how are you going to turn the 24 bit files down to 16 bit. You need to think that through.
Song order I can agree with because sometimes you may have to tweak the volume of a track that is sandwiched between two tracks and if that is changed for any reason then it may not need that gain adjustment after all.
Sweetwater in not in the business of mastering (sorry) they are in the retail business. Maybe you should reconsider a different mastering option.
Leaving that amount of headroom is the correct approach for sure. In
Craig's case if I received a flat lined file that only peaked -6dB I would send it back and tell to remove what ever it was that was flat lining it in the first place. It means that some silly person has heavily limited the music somewhere and that is a form of mastering.