I think anyone in the process of building a house will soon learn that many things are done a certain way for one reason and only one reason, its the cheapest for the builder. This extends to the cheap valve/plastic hose combo they use to connect the toilet, the cheap plastic holders that hold up closet bar, and, of course, using one GFCI to protect every required area in your house. In a previous home, instead of copper pipe, the builder used poly pipe, because its cheaper, probably saved them $500. Cost me $8000 to ripe it out and install copper after it started to fail. None of these changes showed much "professionalism" in my book.
Now builders certainly are tring to make a profit like everybody else, but if you are going to the trouble to build a house, you can make what you want, not what the builder wants. In fact, I bet if you asked the builder how he would do it for a house HE was going to live in, you'd get a much different story.
Hooking up many areas protected by one GFCI is certainly allowed under the NEC, and maybe when GFCI's cost $100 each, it made sense. Today it doesn't, and all you have to do is read this board to see questions like "My garage outlets stopped working" with the solution being, "go to your bathroom on the other side of the house and reset your GFCI."
Separate GFCI's not only give you less walking, but they help you isolate the fault. If the master bathroom one trips, the problem is in, yes, you guessed it, the master bathroom. You will know it didn't trip because last night it rained on your outdoor Christmas lights.
Both methods are just as safe, and both are fully approved by the NEC. You will live in the house, so you need to decide what works for you.