Hey @lhornstra, can you do me a favor? Can you try taking out the boosted model tool (but leave in the Imputation tool and make sure it's configured how you like), and then run the workflow? If my suspicion is correct, you should then see the correct fields coming out of the imputation tool, and you should also be able to add whatever tool you want after the imputation tool and have the fields show up correctly.
My hunch is that since this Imputation_v2 uses a lot of the "Dyanmic" tools (like dynamic rename, dynamic select), it's not able to pass metadata on to the next tool until it's been run at least once, but then after that it should hold on to the metadata so you can keep adding downstream tools as you like.
If that IS the case, I'm not totally sure what the easy fix is just yet. The Dynamic tools offer a lot of power, but sometimes at the cost of metadata persistence so it can be a hard trade-off to make. That said, if we can at least confirm that running the workflow once will generate the correct output from the Imputation tool, and that you can then build your boosted model correctly, we'll at least have narrowed down the issue quite a bit.