Amtrak is under the gun from Congress constantly to make money with their food service and I don't think putting microwaves and frigs on the trains that can be used to heat up and refrigerate passengers personal food would make much sense.
I don't think pushing a menu full of exceptionally fatty and sugary meals on an already bloated and diabetic population makes much sense, but maybe that's just me.
Following that thinking, McDonalds and other fast food outlets do not serve very healthy meals, so they should also provide microwaves and frigs for the use of the public wanting to prepare their own food. Not happening!
Did you bother to consider that McDonald's doesn't have you trapped on-board for days on end? There is no obvious need for anyone to store their personal food in a McDonald's refrigerator or to heat it in a McDonald's oven. Not to mention that as bad as McDonald's is, they still offer fresher and healthier options than Amtrak does.
As far as anyone noticing if you brought outside food into Starbucks or McDonalds I think they would notice and I don't think you would last too terribly long in their establishment.
In my experience most of them won't care one bit that you brought a Whopper into Big Mac territory or vice versa, and I find it odd you're so convinced they would care or even notice. I guess you never worked a job like that or never tried to bring anything of your own inside.