This is a little off-topic here, but I'm not sure it would be any less so on Ask Different or anywhere else. It's one I'll have to try and remember for when IoT.SE makes it into beta, which looks like it will be fairly soon.
So I'll give you a mostly opinion based, research-free, "common sense" answer and maybe someone with a better perspective on the industry will come along with something more concrete.
this option can be blocked by Apple
In a literal sense, obviously yes they could.
However, it will probably never be in their interest to do so. What they have to gain would be collecting license (or certification, or whatever) fees from other manufacturers that are susceptible to this leverage, which might be a large percentage of them, but ultimately that is going to drive the price of the platform up. And as long as those fees remain reasonable, most major manufacturers will be willing to pay them anyway; there's no need to literally extort them.1
Right now, to put it unfavorably, the Apple business model is about branding: They massively overcharge people for technology based on a gamble about human psychology -- that people are willing to pay more for an insubstantial je ne sais quoi because indulging in fantasy goes hand in hand with personal mobile technology and things that access the internet.
A favourable version of this (call it perspective #2, and the other perspective #1) would be that no such psychology is involved, Apple just makes objectively better devices than anyone and so they can set whatever price they want, there is no basis of comparison when you are the best, and it is actually the people who can afford the best and are willing to pay for it that determine what is fair and unfair in terms of price.
In any case, this effect is unlikely to carry over into home automation, and in fact we don't even have to go that far to find an analogy: While they could prevent iphone owners from using any kind of smart watch with the phone made by someone who doesn't pay Apple licensing (or whatever) fees, they haven't done that. Some room full of analysts somewhere has surely already done the relevant research and math abuse here to determine the number of fans that are going to move from perspective #2 to perspective #1 when faced with that kind of "you're being milked" attitude (put another way: Apple must know they are more likely to loose phone customers than gain wrist watch ones).
Further, if the motive behind excessive restrictions on what is and is not potentially part of the Apple Home is greed (and what other motive is there?), this again means higher prices, and for purely pragmatic reasons, people who may be willing to have $50 a month hidden in their phone bill for "the best" may be willing to settle for second place when it comes time to pay upfront for stuff who's logo is hidden from view anyway. Anecdotally, people I know who are diehard fans of the iPhone and buy every new successive model do not seem to carry their brand loyalty over into the realm of home automation, and I am dubious what percentage of people are really that zealous. They have no qualms at all about buying some Honeywell or LG or whatever system. After all, it is not really a religion.
A very significant pragmatic motivation here is going to be mobile integration, and all that takes is a wifi app. Trying to restrict those so that people can't use anything but the Apple Home with the Apple phone is not feasible, meaning, iphone users are free to choose whatever they like. If the Apple Home economy of devices is too restrictive, that will just mean less people buy into it, including fewer manufacturers paying licensing fees, and goodbye Apple Home. No one is immune to failure. Apple already pulled this kind of stunt when they abandoned PowerPC processors, and people with previous generation iMacs were left stranded in terms of operating system support. Could people quickly end up with a bunch of depreciated dimmer switches in their house? Yep.
So if Apple are shrewd (and who would question that?) then they will accept whatever humble slice of the pie they can get here. Trying to exploit leverage they don't really have will make that slice smaller, not bigger.
Then again: Never say never. While no one is immune to failure, some people can afford to fail regularly anyway. But I think the safe bet is they leave that "not certified" option open.
Make sure you check back on that IoT.SE site in a few weeks, I am sure it will get going before the end of the year.
1. Although it occurred to me re-reading this that there is then a motivation for those manufacturers to put pressure on Apple to exclude uncertified devices, which jeopardizes my whole subsequent argument...except I think the real clincher here is the point about the fact that even if Apple Home is made exclusive, they cannot prevent non-Apple systems from creating apps that allow integration with the phone, and that is all most people are going to care about.