seam-gen simply creates a project with sensible defaults, if you want to change them there's nothing stopping you. Simply modify your components.xml and build.xml if you wish to name your rules file something other than the default.
Yes... of course...no problem....
But with each single change to the original ant project, you are getting more and more problems to keep track changes packed in future seam releases.
And there had been quite a lot of changes in the last months.