considering the custom vs stock guitar argument for a beginner I would always recommend buying a stock guitar. Reason being is that at least you know that this is the standard thing amongst guitars for that price range/brand.
For instance if I bought a Gibson SG I would know that it can't replicate the sharp sounds of the Stratocaster, and not the full body tone of the Ibanez. By then deciding to go custom I would be able to say for instance take the LP body, neck/head of the Strat and load it up with two Ibanez pickups and I'll have a nifty looking guitar that looks like a cross of an LP and Strat but that is actually good enough to pass as a super metal guitar.
But asides from pickups there are also considerations to be made on the bridges, electrics to be used, type of wood being used for both body and neck, the neck joint, truss rods, style of tuners, climate that the guitar would live in, action, pickup heights, neck thickness, neck width, neck shape, body finish, fretboard finish, fretboard wood and more!
Going custom should really only be done (imo) when you KNOW EXACTLY what you want!
2005 Martin DX1R Dreadnought, 1994 Fender USA Lonestar Stratocaster, 2005 Gibson Firebird Studio, Aria Acoustic 4String Bass, 25W Fender Champion 110, 100W Peavey Linebacker Bass Amp, Crap Amp, Lots of Boss Pedals