I'm not sure how serious you are and if you're talking about one method of assembly of wood and wires being "better" than another. All guitars are parts guitars, but how the parts are put together varies. You can buy pre-made set-neck parts/kits as well. You can buy neck-thru blanks from Carvin and just glue whatever to either side and cut it into whatever shape floats your boat. Hell, there are even acoustic and carved top kits you can buy.
Building a great guitar using any method is the skill. It may be easier for any schmuck to put a bolt-on neck guitar together, but it doesn't guarantee any of them will be decent regardless of the quality of the materials (individually or collectively). As folks have discussed in other posts, Taylor and Bennedetto built guitars out of old palette wood and knotted pine (respectively). According to the folks that played them, they still sounded excellent...on par with their instruments made of high grade traditional materials (albeit differently voiced). I missed the boat on acquiring one of my favorite acoustics, the Tacoma RoadKing, dreadnaught cutaway with a two-bolt Fender style neck.
For me, Fender showed that for all of old school craftsmanship and artistry that Gibson applied to building astounding early hollowbody/semi-acoustic electric guitars, that all you need is to firmly bind a neck to body. Next, tighten some wire over a piece of metal on the body and tune it up at the top of the neck. Then jam a magnet wrapped in other wire under it and plug it into an amp. Doesn't matter what woods you use, what scale length, or whatever, they can both sound amazing (albeit different, ranging from slightly to HUGELY). Yet despite all of the inherent differences in recipe, in the hands of the best players it gets harder and (more importantly) nearly irrelevant to determine what instrument they're playing...it's about the music they are making.
I like my two Fenders. I like my G&L. I like my Takamine acoustics. I like my PRSes (one set, one bolt on). I like my electric/acoustic bass (bolt on). And I like my two other guits. Neck fixation technique isn't a factor for me, nor is the name on the headstock...I gotta like the sound. So far set-neck acoustics win the overall race (four instruments), but Fender-based stuff wins the electric race with three...if the CE-22 maple top counts as Fender based on the neck attachment, it's a tie!