OP here following up:
I heard back from Empower. The rep explained it as follows:
- Aftertax and before tax money was being deposited as one lump sum into Schwab, and Schwab has no way of knowing the difference
- To extract the aftertax dollars, I need to sweep my entire 401k account back into Empower, extract the after-tax only, then I can put the before tax dollars back into Schwab. It would take a few days for each transaction to happen. I didn't get enough detail on what this means for my funds. I'm guessing that since it's in a tax-protected account, I don't really need to worry about cost basis repercussions? All of the funds are no-fee transactions as well.
- Going forward, I can have the after-tax portion of my contribution stay inside Empower so I can easily roll it over into a roth as I wish. No interactions with Schwab necessary. The rep helped me set this up.
So, going forward the mega backdoor should be pretty easy. I don't really feel like going through the hassle of extracting the ~2k already sitting inside schwab though. I might as well get it over with, since the sooner it's in a roth, the sooner I'm making tax-free gains.
I hope this post will be useful for anyone else who uses a self-directed brokerage (SDB) and is thinking about doing a MB Roth. Talk to your provider first to keep the after-tax portion from getting mixed in with your pre-tax money in the SDB.