I discovered a solution! Follow these steps to apply Auto Layout to Sections:
- Right-click on the Section and click Convert to frame
- Add Auto Layout to the Frame and apply your desired values
- Right-click on the Frame and click Copy properties
- Right-click on the Frame and click Convert to section
- Right-click on the Section and click Paste properties
- Do a happy dance
You will have to redo the process to modify the Auto Layout values, but it should do as a workaround until Figma intentionally adds this functionality.