We'll have to look into what kinds of problems that would cause. I don't expect it should cause many problems, but I remember writing the Config table code a long time ago (6 or 7 years ago) and I remember there was some trouble with the naming scheme then. Of course, that was for Joomla 1.5 and we haven't revisited that naming scheme since. We also haven't heard of the conflict with any other extensions, so it hasn't been a problem.
Can you let us know what the other extension that you're seeing the conflict with is?
Thanks,
Alex