One thing to keep in mind when you use cross app relationships, is your users have to be users of all involved application to see or use the relationships.Do you have any more information about the nature of these apps and why you'd want them to be combined vs. separate?
Regarding performance issues, you'll only see these when you have a truly connected eco-system of apps, meaning with cross-app relationships. TTI's don't generate any relationships between the applications and would not typically cause any long-term performance issues. The only concern with TTI's and performance issues would be an import that has to create or modify a very large data-set.
Blake, I have a recollection that a TTI in fact does cause apps to be in the same eco system. I think that Eric Mohlman (a QuickBase staffer) said that. I am working on a problem now with QuickBase support to get an Application untangled from the eco system so I may learn by the end of it what makes an app part of the eco system. Right now I have an app with no data, no cross app relationships, no script pages and no TTI's and its still connected. I have escalated this with Support, but no answer yet.