Indeed: higher taxes means more gold for them. Guild taxes are based on region taxes, not lord's share.
I had started a Dwilight Banking Guild, though I don't recall the name, but I quickly came to realize that it could be so easily gamed that I never put any effort into developping it and let it die.
Well now I know what to look for. I imagine it will take a while before a branch manager even thinks to commit this kind of embezzlement.