As a professional freelance modeller/designer, I'm often facing this type of comparison. IMHO, excepting material (paint, decals, figures or modelling paste) there is important 2 things you'll pay when you buy a custom figure (or a custom scenery, etc...or any hand crafted stuff) :
the expertise of the modeller
the time amount spent on the project
So the price can vary a lot, and can sound fair or unfair, depending of the client and the modeller expertise
So finally for me a customized fig is more valuable than factory bases. BUT if the bases are pro tweaked, again the "2 important things" has to be considerated on the final price.
Dimitri