I don't think you can really compare those two things... modding a stock guitar and building one from scratch. If you build from scratch you can get every little detail to be what you want... neck shape & radius, fret size, heel cuts & contours... wood type & weight, pickups, hardware etc. Otherwise there's only so much you can do...
The major parts of my thinline Tele came used, untouched but "used" from Poorman and represented a substantial savings over a new neck & body. My total cost on the project was well under $1,000... might've been a little closer if the neck & body were "new" but still.
For under $1000 I got a thinline Tele with a neck humbucker & quarter sawn maple neck. Try getting THAT from Fender, Shur or anyone else! I can hardly count the cost of pickups & electronics in a build since those usually get changed anyway on store bought guitars.
What really drives up the cost on a parts project is finish work... paint. If you can do that yourself or have a friend do it you'll save a lot of money.
And don't expect that you'll be able to just unbox parts & bolt everything together... It's not that easy, not terribly hard either... some basic woodworking & measuring skills are mandatory.