I've been wondering about this myself, and watching the kits hit the market with mixed feelings. Couple of thoughts:
1) I hope they will increase the appreciation among the muzzleloading community for good, historically correct architecture. There are a lot of folks out there, folks that are primarily shooters and hunters instead of builders and scholars of antiques, that only have a vague idea of what really good architecture looks like. I think that Mr. Kibler's kits are going to edge out a lot of the "Semi-custom" market that caters to that particular demographic group, which may have the long-term effect of encouraging certain other manufacturers to improve their product. Maybe.
2) Back when I was a teenager I got interested in building rifles not because I desired by be a gunsmith, but because I wanted a good replica of a Kentucky rifle so I could shoot it. There just wasn't anything even remotely resembling a longrifle available that was within my price range - even the Pedersoli and Hatfield rifles were too expensive and only marginally long enough to count as a "longrifle" for me. Now, while Kibler's kits are not inexpensive, they are apparently exceedingly easy to put together and use very high quality components, which is going to make them a very attractive proposition for someone in the position I was as a teenager (particularly if that someone has a rather more realistic appreciation of how difficult it is to build a decent gun than I did at the time), and thereby reduce what has historically been a big motivator for beginning builders. Whether this will have the effect of reducing the number of people willing to start building their own from scratch or not, I can't say - it is possible that having an easy introduction to building and a good model for subsequent builds will encourage more folks to strike out on their own.
3) The exact impact on custom makers will probably depend a lot on what models Kibler (or others following his lead) introduce. Right now Jim has two rather different kinds of guns - one is a fairly faithful reproduction of a specific NC rifle (albeit in flint instead of percussion), and the other is a very generic "colonial" rifle. At the risk of offending, I have to say that to me at least the Kibler Colonial looks more like a Kibler then any particular original colonial rifle - with that English lock I think it might end up being the brass-mounted variant of the "Early Southern Rifle" that has become so ubiquitous, as it doesn't really look like a PA rifle at all. While I imagine that right now Jim and Katherine are thinking about new models with an eye towards areas that aren't covered by other kits, I predict that eventually CNC kits will end up covering most of the most common rifles - Reading, Lancaster, Lehigh, Christian's Spring/Moravian, Early Southern, Fur Trade rifle, Classic Hawken, Jaeger, Southern Mountain, etc., while the custom makers supply the demand for copies of specific rifles, individual makers, or just more obscure schools. What I hope doesn't happen is that a couple interesting-but-offbeat originals get used as a basis for kits at the expense of more typical examples, the way that the Edward Marshall and Faber rifles have become copied ad nauseum.
I don't think that custom gunmaking is going to go away anytime soon - one of the drawbacks to very precisely machined kits with no wood left to remove is that they aren't going to be easy to kit-bash or customize. Only real options so far are patchbox, decoration, and wood type. While I'm sure that someone, a very skilled and clever someone, will eventually come around and prove that yes, you can make the Kibler Colonial into a stepped-wrist rifle, if you can pull that you can build from a blank and probably accomplish teh same result more easily. I think that is an inherent limitation with kits - the more freedom you have to do your own thing the greater the risk of failure, and the easier a kit is to build the less easy it is to alter.
4) Long term, the market may not be as saturated as some believe. Speaking as one of the much- (and often deservedly) criticized millennial generation, I'd like to observe that there is a very deep-seated dissatisfaction and frustration with the modern world as currently constituted among many younger folks, particularly men. I don't want to get into details of that here, but I do think that there is a lot of interest in self-sufficiency - survivalism, under the name "prepping," has become mainstream if y'all haven't noticed, and here in Hippyville Asheville the Foxfire books are a perennial seller at the local bookstores - and a bit of nostalgia for a time of simpler certainties - I note that the Art of Manliness website is doing pretty well. Some of that is likely to translate into an interest in muzzlelaoders. What we younger guys often do not have is a lot of money, space, time, and/or a background in tool use. A rifle that can be assembled with basic tools in an apartment kitchen and is affordable to someone working two part-time service jobs might be just what this hobby needs to survive for another generation.
Overall, I think that the advent of CNC kits is likely to be a positive development. Making good guns cheaper and easier to acquire strikes me as an undeniable Good Thing. I have to admit that I'm inclined to be grumpy about it, partially out of snobbery (I may be the only person in the world that doesn't particularly care for the Colonial and I'm not thrilled by the idea of seeing them everywhere) and personal loyalty (Jim Chambers coached me through my first gun and Barbie's daughter attends the school at which my father teaches, so really don't want to see their business suffer), but objectively those aren't good reasons to dislike the new kits.