I just ran into this issue with Japan Airways on a r/t. Normally i'd book one ways and not worry about it.. but we have to add a lap child.. and its significantly cheaper to do that on a r/t than one way.

The original routing I found was DFW-TYO-Jakarta then Jakarta - HKG-ORD. However my true routing i wanted was into Jakarta home from Sin. I couldn't do DFW-TYO-Jak, SIN-HKG-ORD since it was 2 open jaws. We live in Washington DC so any USA gateway for departing was fine as long as it was in J. Having the lie flat on a long flight with a 1 year is the only solution. We got lucky though and a few days later ORD opened so we were able to book ORD-TYO- Jakarta, SIN-TYO-ORD return. Both directions have stopovers in Tokyo. I think 3 nights on the way and 2 on the way back