If I think about taking such a flight, the obvious drawback would be how the scheduled flight times coordinate (or don't in this case) with hotel checkout and checkin times, although this might matter less if occupancy is extremely low due to COVID-19. The reality is that regardless of elite status or FHR/Virtuoso/etc. booking, OP should expect to be required to check out long before the time to go to LIS and similarly should expect to spend hours in the early morning in a homeless state before being given access to a hotel room in the SFO area. You can pay for additional hotel nights (on both ends), but many people (or corporate travel policies) aren't willing to do this.