I think that twigging and tweaking is fine in a home-made adventure. Odds are that the ad-hoc changes you are making are ones that enhance your game, or at the very least let you gloss over some of the weak aspects of your game. In any case, you will only be making changes that fit your groups style of play so you can't go too far wrong and have no one to blame but yourself if you do. I have no problem with that.
Published adventures are a bit different. I expect a certain baseline, a standardization in the rules-- the same standard I have deviated from slightly for my house rules, or my style of play. If an adventure uses a different variation of the rules then I will have to do even more work than usual -- I already know the implications of my house rules on the core rules, now I have to rethink them in terms of a new development. I expect this sort of thing if an adventure is clearly marked as a Scarred Lands adventure or an Iron Kingdoms adventure, but if it is suposedly generic, I expect it to be generic.
Now, sometimes I think that rules tweaking can add flavor, but most times I just think that it is lazy design. (Again, this only applies to published adventures where the author is being paid so *I* can be lazy.) The Stone Giant with +12 in craft --and I'm not sure why you would need that number exactly, but I'll get back to that -- seems to be a bit problematic. But not really too much. I wouldn't go with expert levels, I would use commoner levels, they have Craft as a class skill as well.
Eight levels of commoner would only add +4 BAB and +2 to all saves, and barely enough skill points to max out craft. Technically, this would increase the CR of the giant by 7, which is really misleading if the PCs are just expected to fight it. If anything this is where the ad-hoc tweaking comes in to lower the effective CR. (But state explicitly what is being done, so the DM knows that it was done deliberately and why.)
If you want to compensate for the higher BAB, you can lower the Giant's strength by four points. Only that much, though, because your nerfing the damage as well. Not all giants have the exact same ability scores; those found in the MM are just averages and norms. Or if this giant is primarily a crafter rather than a warrior, don't give him a club, give him a big solid oak chair. He'll be -4 to hit because he isn't proficient in fighting with chairs. That will cancel out the extra BAB from the commoner levels, but the size and sturdiness of the chair will justify a damage die simmilar to that of a club (and besides, most of a giant's damage comes from the strength modifier anyways).
Now, this is of course taken out of context, and the problem might be more or less difficult to solve depending on the actual context. Why +12? Is it just for flavor? Will +4 suffice? If the stone giant needs to be able to create a specific item for the players and the DC is 22, then a +12 modifier would allow the giant to make the item at the first attempt by taking 10. Fair enough. Changing the item that the PCs need so that the DC is lower, and switching off monster skill points might be easier than adding commoner levels, though. Or at least lowering it to a point where one commoner level will do the trick (no BAB, or Save bonus, 8 skill points) will really just save a ton of hassles.
Just my two cents... well, 4 cents maybe, if you go by bulk rather than quality.
Cheers
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