Here are some thoughts. (Some inspired by what other members have written above)
A good guitar needs to be well set up. But a poorly built or assembled guitar even when set up still lacks a proper foundation to be good or great.
You do need to know the science and techniques involved to end up with a good or great result, but the art is in how these are applied, and the care put into the final result.
Definitions
Set up
But what is meant by set up. I would include in this final adjustments such as truss rod, bridge and saddle adjustment for string height and intonation. Also, pickup height etc. This has nothing to do with assembly or building, but is something that needs to be done and at times redone over the life of an instrument. This is a skill that I think all players should get familiar with. Adjusting the height of a nut is needed for good set up, but many players might get help with this, as it requires tools and a certain degree of extra skill.
Final assembly
This is where a set of finished parts are put together, the neck screwed onto the body, the nut fitted, the bridge and pickups fitted, the strap locks attached etc. (this is not in exact order of sequence) but it is what many assembling a Warmoth with a finished neck and body are doing.
Assembly does not really in the opinion of many make you a builder, though a builder will do assembly at some stage of the build process. So we could say assembly is an element of the overall process of guitar building.
The attention to detail here can make a big difference.
Finish
This is of course applying things such as lacquer, poly or other finishing materials such as tru-oil to a body and neck.
Initial assembly
This would be either a full assembly or dry assembly to check for overall fit. With a full assembly, a disassembly would be done prior to finish and final assembly and set up.
(note all Warmoth and related parts should undergo a dry assembly prior to actual assembly or applying any finish that may be needed to check for fit etc, especially if something is not to spec and needs to be returned to be corrected or replaced)
Body and neck manufacturing
In the case of Warmoth, this is what you are buying. Parts that are in various possible stages, such as fully finished and routed, or a body or neck blank that needs more work done by the end customer.
The more that Warmoth has done, you will have a set of parts for assembly, the less you will have to do part of the job. Either way, it should be realized that putting parts together is not always a join the dots process.
Fretwork
Warmoth necks can be obtained already fretted or without frets. I personally think they benefit from further work where needed to take things to another level than will be obtained out of the box. But this is more skilled and requires the correct tools, so is something that many either do not do, or farm out the work. A few of us take a pride in doing this work.
Wood
Not all wood, even of the same species, is created equal. Do you know the difference between, flat, rift or quarter sawn for example and why you might use one over the other for example?
A maple neck with rosewood board from one maker is not the same as a maple neck with rosewood from someone else, for example. For that matter, no two necks with similar specs are the same or identical, they are merely similar.
You then have how much wood is rejected due to even slight defects such as a mineral streak. Some defects may be aesthetic and not really have an influence on playability, but a manufacturer will set the standards they are looking for and may even end up cutting a neck and rejecting it for a flaw that did not show up before cutting the neck. All of this goes into the final cost someone might pay for a guitar or a part. What one manufacturer may reject may still be in the tolerance of another manufacturer offering a lower cost product.
Design
How much of a guitar are you designing, you might choose the pickups, the colour, hardware types etc and this is all under the heading of design.
Making tweaks to an existing design such as a Tele or Strat by changing or improving the dimensions and hardware choices or tweaking the shape of a contour could fall into design.
However, the basic design of a Strat or Tele, or its architecture if you will, was created or designed years ago and design tweaks do not change the basic architecture.
Playability versus Aesthetics
Some might not care how something looks as long as it plays well. Or in the case of a "coffee table" type build, exotic expensive woods may be chosen, but these may be no more playable or have better "tone" than a plainer finish and reasonably priced woods.
Summary
Can someone take a set of Warmoth parts and make something great? Yes
Can anyone take a set of Warmoth parts and make something great? No
Can any reasonable player with basic tool skills make a good instrument from Warmoth parts? Yes, the potential is there to do that.
If I bought the best parts I could and gave them to a new assembler or to John Suhr or Ron Thorn, for example, my money would be on John Suhr or Ron Thorn, producing something great from what they were given.
To use an analogy it is not just the recipe, or the ingredients, or the tools, it is the skill and art of the chef that makes a great meal.
Click on the Welcome to the Forum thread link in my signature, there you can find links to lots of useful threads where further knowledge may be gleaned for taking things to the next level.