I think I don't fully understand your problem but if you make a company shareable over multiple companies, you don't need that company column. Further you have to extent all queries (and indexes) with a company column. Last but not least the Baan architecture gives you the possibility to have a different package combination for company A compared to B. So, from many points the approach Baan has is preferable compared to having an additional company column.
BTW: this post has been made on my personal view. My employer might not share my point of view.