Since all members of a race have the Charisma penalty, they're all making opposed Diplomacy checks and such against eachother at the same penalty, so they're all doing equally poorly bartering with eachother or whatnot. Just like how a halfling's +1 attack bonus for size is irrelevant against another halfling because of their +1 size bonus to AC for being small. It doesn't really affect them much amongst their own kind. And just because a race is gruff, blunt, and ornery, like Dwarves, doesn't mean that they're bad at noticing other folks being the same (no Wisdom penalty, so Sense Motive doesn't suffer, but that's only used to oppose Bluff anyway).
And some people are just naturally ill-tempered, rude, or anti-social in real life, so of course it's possible that a race may have similar tendencies instinctively as a whole. Even though Dwarves may suffer a Charisma penalty that affects their dealings with Moradin (through whatever means), Moradin created them to be of such a mind, so he isn't likely to be fazed by it. In the same way that dragon deities don't mind the impiety and enormous ego of their draconic creations, because they made them that way, and they wanted them to feel superior over other creatures. So they don't take offense at such behavior most of the time, and aren't likely to smite their followers for being just as gruff or egocentric as they intended.
Remember, Charisma is a combination of beauty, slyness, persuasiveness, ego, and force of personality. Dwarves are gruff and a bit ill-tempered, but they are also very communal and clannish, very close to their community/family, and do not have particularly distinctive personalities individually (otherwise they couldn't be so accurately categorized as being generally blunt, gruff, and ill-tempered). Orcs/Half-Orcs are horribly egotistical and selfish instinctively, and don't much care for others, let alone those who get in their way. Orcs/Half-Orcs are naturally less cooperative and compromising, and don't care for social mores or taboos, compared to humans.