It does matter, actually. Imagine this:
Dwarf Fortress becomes more and more complex, receiving the occasional interface updates just to keep up with its features. At some point, someone comes up with a really powerful program using memory hacking. This program is so good, no one but the hardcore ASCII-forever-and-Toady-for-prez (humour intended) players can or want to play without it. 75% of the userbase (hypothetical number) is then reliant on this very popular 3rd party application that breaks pretty much everytime the game is updated, generating enormous pressure on both the modder (who might not mind doing it) and Toady (who probably minds) to keep things running smoothly, even though they won't cooperate directly.
Not a very good situation, really. So there has to be some sort of limit so the situation won't escape Toady's control. There has to be a line people agree not to cross with their modifications/applications, otherwise the only solution would be banning those methods altogether. And if DF became impervious (or at least resistant) to memory-hacking only after the userbase started relying too much on a third-party application, the backlash would be catastrophic. Think about the "THIS SUCKS!" topics you see every time something is nerfed in any game (such as WoW). We'd then see something like that over here, and I think I'm safe to assume no one wants that.
So, yes: discussion on what should and should not be done must happen early in the development. Players absolutely hate it when something they like is taken away from them (for whatever reasons there would be), so it's better not to let them become spoiled with things that might need to be removed later on.