We have been playing with submarines using fuel on LT50 (2.5 game) for some time now and it looks like this stuff is working almost perfectly or perfectly. I haven't seen a single real issue with the subs. The only issues have been few times with slow goto (1-2 sec delay) and the need to control the sub with cursor keys when the fuel runs out and there is no way to return to the base. Then again it's the same for fighters and missiles so it's not really that serious. I can also only blame myself for taking the submarines to suicide missions
I haven't tested returning back home automatically because that's a special case and there was no need to do that with 23h turns. At least no need for me.
Planning and discussing Freeciv Longturn gaming