As far as i know, the appearance changing costs is something that's also in base NWN. Crafted items' item values are significantly lower, however. (Maybe just even 1? Correct me if i'm wrong)
The cost to change an appearance is tied to the item value of said items and i believe this is also present in base nwn. There's mods out there that do make it free however, so it's likely possible to be changed. I've never found the gold cost to change items to be of any consequence however, nor has it ever really bothered me personally
It's mostly inconvenient for early-game characters who have no need of a gold sink. If you're level eight, in the Outskirts, and you get a piece of armor that is useful to you at this point in the game, it may cost you 5,000-10,000 gold to get it to look how you like. It might provide you one more AC than you'd get with a suit of crafted full plate armor.
Once you're like, level 20, or level 15, this isn't such a huge issue, but for most classes, there are crafted alternatives that once enchanted, are just better anyways. The only people who tend to get stiffed on this front are spellcasters, who do not really have a crafted armor equivalent because they need spell casting slots. For Paladins, Fighters, Barbarians, Rogues, and otherwise, crafted gear is usually sufficient.
However, at the late game, it doesn't matter all that much for them, either, because it's easy to come across Gold, and it's a one-time expense. So it mostly inconveniences the kinds of characters who don't really have a need of a goldsink in the first place.