The truth is that you can use whatever you want, wherever you want. Your quilt, your way.
Many longarmers in business will use something such as BottomLine, SoFine, or another thinner thread or prewound bobbins to save money/time (time is money). Most longarmers like to use a blending color to the top thread, so that pokies, tensions issues, etc. don't show. One other thing, if using something expensive like KingTut on the top, it costs twice as much as necessary in thread costs than if you use something more economical such as BottomLine on the bottom - so that's another reason longarmers frequently use a different thread on the bottom.
Me, I like my bottom thread to match my backing - I think it looks so much better than multiple colors on the backing. So, I use whatever I want on top and match my bottom thread to the quilt backing. (I don't have tension issues.) It's all a personal preference, so you can do whatever you like. That's what I do!
Just FYI...and my knowledge/opinions :)
Debbie in Austin