That's how my first Warmoth started. I could buy a Warmoth the way I wanted, or spend more money modding a Fender. For an off the shelf Fender you would settle for, and not choose, neck radius, nut width, scale length, fret size, neck construction, tuner style and size, neck/fretboard/body woods, pickup routing, bridge style, finish, etc. In short, everything.
It if matters, lately I've seen more aftermarket Fenders than Fenders. My guitar player Warmoth necked his Strat. Another friend has an all Warmoth Strat. Another friend has a Warmoth necked Tele. Although not Warmoth, another friend has an Allparts bodied Strat. I saw a show recently with a guy playing a Warmoth Tele.
It seems to be a consistent philosophy that your happiness with your Warmoth purchase will be limited by your choices and how well the final setup is done. Assembly is not a setup. Have no fear about the Warmoth quality. They don't stay in business and have repeat customers by producing subpar products.