Anyone know the long term consequences of using a standard "Home Depot" ballast in a walk in freezer as opposed to more expensive low temp start type? The cheap ones seem to
work.

You must be lucky. I installed a Lithonia standard fixture in a warehouse that only got as cold as 50 degrees and had to replace it in 2 weeks with a H-O ballast. Are you sure that the ballast isn't a H-O one?