If you understand with a housing loan, that you are essentially paying interest of a loan first. Even though the amount you pay each month may remain the same, the proportion that goes towards interest compared to principal will fluctuate over the life of the loan.
The miracle of compound interest in an investment is how it grows exponentially when the interest is reinvested.

Compared to some investment decisions, the decision of using a Custom Builder vs Project Builder may actually be quite simple.

Let's compare the difference and after the complexity of dealing with banks and finance you may be pleasantly surprised the next decision may make itself for you based on a few key areas.

Do you have to visualise the end result?

Of course you need to know what your place is going to look like.
A Project Builder may be able to give you an example. A display home.

A Custom Builder may also be able to give you an example but on a computer screen or as an architectural drawing.

So the question may be can you visualise the end result? A display home is in a different location and a computer screen or drawing is an artist impression.

How flexible is the builder with variations?

Anyone who has watched a program like Grand Designs is familiar with the inevitable variation. A variation is where a change is made to an agreed plan. There may be a charge for this.

Variation definition:
A variation (sometimes referred to as a variation instruction, variation order (VO) or change order), is an alteration to the scope of works in a construction contract in the form of an addition, substitution or omission from the original scope of works.
https://www.designingbuildings.co.uk/wiki/Variations_in_construction_contracts

The point here is if you have a good relationship with your builder, the process of being charged for a variation is going to be easier.
If you are someone who avoids being 'locked in' developing a good relationship with the builder is going to be very important.
You do not need to be best friends but you do need a good working relationship.
Some responsibility here lies with a client. A Pixie Skase approach may cause issues - Pixie famously would request tile colour changes at Sheraton Mirage.

How unique is the location?

If it is a "flat earth" new estate location the approach will be different to a challenging block with a slope, or is quite narrow.