It's more the encouragement part that I was referring to. 4e, for example, was written in a fairly authoritative tone, which did not encourage house ruling.
I disagree with this because I have a different perspective on it. I got a mechanical ruleset and just because of that I was going to tinker, just like I had been doing for years before with any other system. I think the huge encouragement for me was that 4e presented a base framework that was very robust, and quite transparent. It was not trying to hide the mechanics in obscure flourish, making it very straight-forward. For that reason it was imminently tweakable (because I could easily see what might be a knock-on effect since it was not hidden) and it was robust enough to bend without breaking.
That and a constant stream of updating the rules IMO resulted in groups waiting for the official line before instituting changes. Having a very transparent ruleset meant that it was easy to see how changes would affect the game, but, the way the game was written, DM's weren't really being encouraged to start kit bashing.
I can see that though I disagree. When I have a robust system that works I have less need to house-rule. I don't think that is a discouragement so much as it falls under the umbrella of "if it's not broke, don't fix it." That is a matter of taste. In the case of 4e my house-rules were to implement flavor adjustments, not to "fix" rules. The rules worked OK right out of the box, but if I wanted certain flavor I had to tweak them.
For example, adding a point based casting system outside of the AEDU framework would be a ton of work. Thus we get the 4e psionic rules. It could be done, sure, but, it certainly wasn't encouraged.
But the point is that once you have the psionic rules you don't have to reinvent the wheel and design from the ground up a point based casting system. You can take the psionic rules and tweak them to get that mechanical effect if that is what you are after. In 3e designing, from the ground up, a point based casting system with just the core 3 is also a great amount of work. However, once the designers gave us the psionic system and alternate casting systems in Unearthed Arcana, Magic of Incarnum, there is no need to do so. you can use one of the ones provided, or tweak one of the ones provided to do so.
Heck, removing the grid, while possible to do, wasn't exactly easy. Nor would futzing about with the initiative system. Just to name two spots where house ruling could be a chore.
Interestingly enough I've done both with hardly any hard work involved. So IMO it is a matter of system comfort. If a DM is comfortable with the system then house-ruling all these things is not really hard work. The system makes it easy to do so because it is transparent in a most areas. However I agree that in some areas the level of work might be involved and since for most instances the game works without the adjustments, then why go through the trouble of doing so.
Again, I'm not saying impossible, just not encouraged. And not encouraged to the degree that 5e is trying to with it's boatload of optional mechanics.
The other side of that coin is that even the optional stuff should be seamless when implemented with the base game assumptions. If the optional stuff will "break" the base assumptions I would expect that the designers would provide you with those caveats.