In order to preserve the Checksum for everyone, all of the features are in the code of the patch, the DLC just determines what you can actually play as. But the DLCs can't really restrict access to the new Colonial Nations system because that would pretty much kill a ton of the gameplay for France, Spain, Portugal, and England. As those are some of the major powers, restricting their gameplay just because you haven't bought the DLC would be a bad move.
I'm not sure this is true - gameplay need not be 'restricted' as such for those nations, it would just be as we have now.
Surely the "no colonial nations" behaviour is simply "colonisation as per 1.3 and before." The old colonisation mechanics will still exist in the game. The existing mechanics will still apply in Africa, Asia, Australasia. So it's not that all colonial mechanics are being completely replaced with colonial nations. It's that they're being completely replaced in the Americas.
Therefore it seems easy enough to have a toggle, "Americas use new mechanics" versus "Americas use old mechanics". So it could be a DLC-only feature, if they so chose: without DLC, colonisation would run as per 1.3 for the whole world.
It is ridiculous from technical perspective because they would practically have to balance each new feature twice: one from those with CoP and one for those without.
But this still replies regardless, no? We are pretty sure that the new Native American features are definitely CoP only. So if you have CoP and play natives, you get them; if not, you don't. That's all fine because it's internalised. But what if you play a colonising nation? If you play Portugal, Spain, England, and you go colonise the new world, and you have CoP, you meet a bunch of nations using new mechanics and new features; federations, migrations, different tech, etc. If you don't have CoP, you meet a bunch of nations using.. well, the current mechanics I guess?
So it still has to be balanced for both scenarios.
I agree that your point may still be valid in that
the more features they have to balance for both, the harder. But it's not that they won't ever add new balance-changing features to the expansion. If they did that too much, what would there be in the expansion to encourage anyone to buy it?

There has to be something new, and meaty enough to be worth £15. Just random map generator would not be enough to justify that price.
Note that in all this, I'm still of the view that colonial nations are probably going to be available in the patch and not be a DLC-only feature.
But I don't see any huge technical challenge with making it DLC-specific.