xchat does not have an option to set geometry. This makes it difficult to layout windows automatically from .xinitrc. See xterm's -geometry option for how to get this right (so that -geometry +0+0 works properly with twm).
IMHO, this is something the upstream maintainers should handle. It's more of a lack of feature than a bug IMHO.
You can set the geometry for xchat in it's config file, or via the "Settings -> Setup -> Main Window" in the UI.