Blender 2.6x and 2.49 are very different and still quite incompatible. Lots of 2.49 scripts won't work with 2.6x for example. In fact, it's quite common for users to have both versions installed. Blender 2.5 had its own slot, so should 2.6. Reproducible: Always
The problem is that 2.49 is not maintained upstream. And since it has problem building with modern tools and libraries, security issues, QA issues, etc etc etc there's no way we're going to maintain more than one version of Blender in parallel. So, no slot.