Flame war aside, I think there are some good points in this thread.
Perhaps someone can clarify two points:

1. Is it kosher to add columns to other modules' tables? E.g. Is it ok
for comment to add it's statistics to the node table. Similarly, I
could imagine the stats module would want to add summary information,
and perhaps other modules as well.

If one module is core and one is contrib, then it is not kosher (IMO). Actually
it is not the sanctioned way of doing things, but no one stops a module
author from doing this or a site from having their own "schema fork". There
are consequences when upgrading, and they should be prepared to live
with their decisions.

If both modules are from core, then why not? We avoid the performance
issues caused by having two tables, and are actually more normalized
that way.