Sounds like your builder is planning on a lot of crown molding if he is saying you have 42" + 7". Crown molding can cost as much as cabinets, and is purely decorative, rather than providing utility. However, stacked cabinets can also be very expensive. Maybe he is saying if you have 42" cabinets, a beefy soffit or crown molding will still cost less than stacked cabinets. 49" tall doors is a terrible idea. It'll look odd, and unless the doors are top-quality, will rack over time. This builder appears not to know that, or doesn't care.
Here is how you should figure it. You have a 9' ceiling = 108"
Floor to top of counters = 36"
Top of counters to bottom of uppers = 18"
Crown = 3" (you can have a thicker crown, it depends what look you want).
If you want stacked cabinets, assuming a 3" crown, that leaves you able to do 36" + 15" stack, or 39" + 12" stack, or 33" + 18" stack.
Q