I finally figured out how to accomplish this, and I'm convinced that it's not possible in HD Pro 2017 with Automatically Rebuild Foundation enabled.
To minimize variables which might be confusing the issue, I created a very simple plan from scratch which reflected the essence of what I was trying to accomplish: Stepped Foundation - A.plan
I immediately noticed that the foundation, even with the default settings, wasn't rendering properly with this configuration. Notice how the floor framing is exposed on one of the walls:
I also noticed that many of the Room Specification > Structure settings wouldn't stick anymore. I'd change them, and then immediately return to the dialog to see the old settings remained.
I then proceeded to manually edit the foundation, and was able to accomplish the stepped foundation I needed: Stepped Foundation - B.plan
Here are the Structure settings for the left and right foundations:
Here are the Structure settings for the rooms above the left and right foundations:
I then re-enabled Automatically Rebuild Foundation and it undid all my work:
I tried plugging the Structure settings above back in, but once again they wouldn't stick.
Hopefully this info is helpful for anyone else who's running into this issue.
If there is a way to accomplish this with Automatically Rebuild Foundation enabled, I'd love to learn how.
Thanks!