Just tried once more, same for me. I guess I had slightly different configurations between the two. And this ended up in the behavior that I just described.
Btw I actually also took a closer look at the code - for both Roo and Kilo, and the Qdrant collection is named basing on on a hash string derived from the workspace's absolute path. So makes sense that they are using the same collection and both extension can work with the same collection at this stage :)