Mutagens can change any gene, and the gene is totally selected at random. So yes, they can change even the dominant color and marking of an animal.
It's arguably better than trying to find wild stock with the gene, because there's an equal chance for everything, rather than say a 5% for X gene. But the cost is that it can (and has) totally ruin(ed) the pet in the eyes of the breeder applying it.
I'm in a situation similar to yours, where I'm trying to breed for a color, but because of the random nature of a mutagen I've chickened out on 90% of the individuals I probably should use it on, simply because if they lost their color gene they'd be pretty much useless to me.
But, in the one or two I've used, my outcomes haven't been so bad, really. Neutral, I should say. Used one or two on this guy: Whitegrass and it changed his recessive dilute to piebald (kinda meh, since I'm breeding for diluted) and his normal teeth to double incisors (also meh, since his blunt teeth are now dominant). I really like his breeding recessives, but his flaws make breeding with him a total crap shoot unless you get lucky, like with his son, Othello.
I thought there used to be a mutagens thread around here somewhere where people used to share their success/fails with them. Gonna try and find it.
Edit: Here it is, http://beastkeeper.com/thread/658
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