Each builder is different but I can answer a few of your questions:

More and more places have HOAs, will still fall under some type of county restrictions
Usually fence not included but can be negotiated into price
Good luck
Typically yes, depends on several factors but if you have a septic and leech field, that will play a role in home location
Depends on location, just remember a well is great until you run out of water and have to drill deeper or replace the pump. Average $100/month water bill, put that away into a saving account for the time you need it. Septic is usually every 2-3 years to get pumped.
Depends on location
Almost always a deposit. We heard various deposit amount from $10k-50k
No idea
Some builders have a design center that is all inclusive and you pick everything there, we had multiple places that we had to pick cabinets, granite, flooring, paint, shingles, tile etc.
This is where you want to be exact, get everything picked ahead of time the way you want or make sure there is an allowance (like $5000 for granite countertops and $10,000 for cabinets etc) built into the contract. If you go above those allowances you pay the difference. This can be done for any contract work like your fence, septic, well, etc. if it goes that deep you will want to call around on prices, and negotiate in contract that you will have option to pick different contractors to do work.
It can be set, but usually not. A base price is typical, but extras can add up.

If you can pull it off, and if I ever had to build again....I would buy the land and own it out right, subcontract out everything myself and be present for everything. Write your own contracts with each subcontractor and if they don't perform, they don't get paid till it's right.