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If I understand you correctly, you're trying to solve a very difficult problem that you don't need to solve.
The problem that you're trying to solve is how to manage a situation where you have many different components which have cross dependencies and are released on independent schedules. That's a very hard problem, not the least because each component needs to know about what is happening with every other component that it might care about.
But you don't need to solve that. Put everything in version control and have one release cycle where you release everything. Every time. Now all of your version dependency problems go away. Rather than needing to know all of the combinations that might work together, you need only know that this combination works together. If you set things up carefully, the entire application can live in one source tree, allowing you to have multiple copies on one machine that do not interact with each other. (Configuration modules that set the right path are a good thing.)
Most people don't do this with modules that aren't under your control, such as a DBD. The solution there is to rely on modularity. Make sure that every production machine has the same versions of everything. If you want to upgrade a key module, make sure that the old and the new work the same as far as your application goes (regression tests are a good thing here), then switch only that module, everywhere. If the part of the API that you're relying on hasn't changed (generally this is true, though you need to test this assumption), then it doesn't matter at the point of rollout whether you're using the old or the new.
The motto here is "work in reversible and independent changes". That way each change can be tested and rolled out. If anything breaks then you know what it was and can easily roll it back.
But if you want to really be paranoid, what you can do is have a special subdirectory for external code. And then everything can be in there. Personally I don't like doing that though, since I've had worse experiences with binary incompatibility between machines than with moderately careful system administration as described above. (For instance I've been left with no incremental upgrade path between using different versions of Linux - which is something that I can't put into source control.)
In reply to Re^3: What is YOUR Development Process?