Plan your custom home to use standard sizes for finishes such as flooring, carpeting , doors and windows. All these products come in common widths and sizes. Work these into your plan to avoid the cost of custom manufactured goods. Larger custom homes cost more to build because they require longer floor spans and ceiling joist.
Higher ceilings call for more drywall and insulation, paint and trim. Doors and windows are usually larger, fancier and more expensive. Kitchen cabinets are also larger. The increased weight of all these materials means the joists and I beams must be thicker.
Choose fixtures and finishes that are less expensive but still good quality. It is not necessary to always have the most expensive product just because you can.
Look at the use the item will get and choose the item that will do the job, give the look you want but not be more than you need.
Some items that can be downgraded without compromising the look and quality of your cusstom home are prefabricated cabinets, hollow rather than solid doors. If trim is to be painted you do not need high grade trim since it will never be seen.