The servicing aspect is critical.
When we're in that phase of excitement about a new watch, we tend to forget about it.
I understand your horror story. I had a similar experience with a brand that is one of the most prominent independents (although probably a bit too big to be discussed on this particular board, but very well known and still very independent). It was one of his simpler watches. I thought it might be running slow and it had been a while since it had been serviced. So I brought it by the boutique. Not only did I get the typical forecast that it would be four to five months before I saw my timepiece again, but I was informed that the servicing would cost about US $2,500 (in excess of 10% of the original price of the watch!). Mind you, this is a watch that really didn't have anything wrong with it, was in mint condition and merely needed a regular look-see and maybe a minor adjustment. Well, to paraphrase Ayn Rand, I uttered the word "No." (Annoyingly, the boutique wouldn't take "no" for an answer at first and, after engaging in some very patronizing "advice" to me, finally deigned to return my property to me). There was zero flexibility, zero discussion, zero willingness to work with a customer. I have purchased 2 timepieces from this manufacturer at a cost in the neighborhood of $40K; there is zero chance there will be a third.
On the other hand, we consumers must set our expectations reasonably. We know these smaller manufacturers are limited. We know that you will never, ever (I don't care how good a watchmaker you are) get the same level of ultimate reliability in a small-run, hand-made production as you will with much larger runs of watches. It is simply not possible from an engineering or statistical standpoint. So, in a sense, but going with the smaller independent watchmakers, we are signing up for this kind of treatment. And, since they are smaller, have less capital and are less diversified, the risk of going out of business is always there and always greater than it would be for, say, Rolex.
At the same time, the purchase cost of some of these limited-run, independent pieces has skyrocketed. So the risk being borne by the purchaser is now that much greater.
Seems to me that the only real alternative is third party servicing. Obviously this is hugely risky if the buyer of the watch attempts it on his or her own, as the buyer will typically not be able to tell ex ante whether the jeweler knows what they are doing (and the smaller the manufacturer, particularly if the movement is in-house, the higher the risk of ignorance). To the extent the movement is complex or unusual, the risk is, again, exponentially higher. And of course, whatever "warranty" you might have from the manufacturer will be instaneously voided (I personally discount this latter risk, as I don't ascribe any particular value to these "warranties" in the case of the smaller houses).
But it seems to me that the smaller houses could (consistent with the antitrust laws) -- and should, in the interest of providing reassurances to current and future customers -- get together and work on putting in place a network of third party certified workshops that could be called upon by customers to do, at the very least, the more routine or simpler repairs (periodic "tune ups" and cleanings). This would also have the salient effect of freeing up manufacturer resources to make new watches and develop new models, and it should enable the cost of at least the more usual types of servicings to be reduced. Rebuilds and the like would continue to go back to the source. We tend to treat these timepieces are sacred objects and most of us would blanch at the idea of sending one anywhere but the manufacturer to be attended to -- but the fact is that, with proper training and documentation, many of the routine tasks can be safely undertaken this way.
I agree with your premise that unless the smaller houses deal with this problem in some way, it could come back to haunt them.