I'm no pro, just your average joe shooter so take this for what you will.
I don't think one is anymore or less accurate than the other. BUT, if you are going custom anyway, I would never do a 338 Lapua that wasn't one of the "improved" versions. IMO, an improved 338 Lapua is well worth any extra fuss you may think it involves.
If you have Kirby Allen build you one of his 338AX you not only get your dies with the build but you can buy fireformed 338AX (338 Lapua improved) brass from him. If you want to fireform your own that works too because the standard 338Lapua loads will easily shoot M.O.A. they just won't be quite as fast.
For me, a 338 Lapua Improved would be a no brainer and kinda the best of both worlds because it would still shoot factory 338 Lapua ammo very well.