PEX design question

I am in the planning stages of a repipe of my single story house with mostly old galvanized pipe. As I look at the 3 main designs (trunk and branch, home run and remote manifold) I am wondering why there aren't very many suggestions of more combinations of PEX. I have only read about some different combinations here.
I have a two bathroom main house of about 2000 sq feet. I have a central manifold location picked out in a utility room next to the water heater. The kitchen is directly above and each of the 2 bathrooms are about 30 feet to each side of the manifold location. I have a detached guest house 20 feet beyond one bathroom for a total distance of 65 feet from the main manifold. It houses our only washer and dryer and a sink and shower. All of the existing plumbing is beneath the house in an easily accessible crawlspace. My main question is why would I not want to run a hot and cold line from the main manifold to a hot and cold flow through manifold at each bathroom? Could I expect pressure loss as compared to a home run system? It seems like much less of a hassle with much less wasted material. For the guest house I plan to either tie the new copper hot and cold supply lines into the flow through manifold of the closest bathroom or run those lines directly to the main manifold due to distance-about 60 feet. Again, at what point does distance to a fixture become a consideration? My current pressure to even the most distant fixture is good. I plan to upsize the existing water main from 3/4" to 1" flexible copper as much in conjunction with this project as possible because I am unsure of its age. Thanks as always.

IMO you can't beat homerun with a manifold, so I'd use one in each house. And I'd run 3/4" to water heaters and 1/2" PEX to all fixtures except toilets.

I would not use flexible copper, I would use 1" 160 psi rated PE pipe.

And don't forget water treatment equipment like a water softener.

That makes sense. What would you run to the toilet 3/8"? The current water main comes directly out of the ground where it meets the front of my house goes up about 10" makes a 90 degree bend and penetrates the front wall into the crawlspace. Would you use 1" PE and transition to copper for the above ground part that enters the house? I live in AZ and am not worried about extreme cold and grounding is not a problem. Thanks for the advice.

I'd run PE all the way to the manifold.

If your main line from the street is metal, it may be used as the building's ground, if so and you go to plastic, you need ground rods and proper grounds.

When we say PE do we mean PEX¿ Here they sometimes run gas in PE.

1/2" to the toilet not 3/8"

No, polyethylene (PE) pipe for potable water use. PEX is a type of polyethylene.

so, why not 1/2" to the toilet?