To be honest, I usually just prep an extra altar for most of my builds because you're almost guaranteed to get an altar you want, and more variety doesn't ever hurt. In fact, if prepping a god had no downside, I wouldn't mind, since you're already giving up the extra altar... all that the prepping penalties do is make it so you can't reasonably prep GG. On the other hand, that's because my playstyle involves a lot of preexploration, so I can see the god spawning next to you being helpful to conserve blackspace.
With the Heretic, the fourth altar is better than anything else because because the entire point of the character is to trash as many gods as possible.
I don't think a nerf like that for Curious VGT is really necessary. All that would cause is more scumming, but the final build for the Heretic won't actually lose much power. The thing about VGT is that since it has all 9 gods, the Heretic is inherently much stronger than usual. I don't doubt that this is true even if the gods spawned per tower. This nerf would make the middle towers much more difficult, and depending on which gods spawn if you get unlucky you won't be able to clear some towers at all (Curse Bearers before EM or TT, for instance, will lose you a lot of mileage with those two gods). So basically, just make the dungeon more RNG heavy rather than actually being more difficult... I'm not a fan of the idea, myself.