Used fuel weighs more than the raw fuel, it’s just outside your vehicle in the typical use case. As you have shown, a typical assumption made with fuel burning vehicles is that disposing of the effluent is free and you can just throw it overboard.
In terms of measuring performance of the aircraft, you do indeed just throw it overboard. Obviously the energy system as a whole need to take into account the dumping of hydrocarbons into the atmosphere but I believe the parent commenter does that by suggesting synthetic fuels created through carbon capture.
Anyway, my point is just that when comparing two aircraft, and their fuel sources, it’s probably worth just comparing the closed system of the aircraft and measuring the environmental impact of fuel sources separately.
It's also important as most long range airliners take off with more fuel than they can safely land with. The air frames are very heavily optimized as every pound matters. If you always landed with the same weight you took off with, you'd end up needing to make the landing gear and surrounding structure significantly stronger to prevent excessive wear over time.
My point is that achieving energy density parity with jet fuel isn't enough to make battery powered intercontinental flights viable. Such an aircraft will not be able to get to its destination. You can't get a fair comparison unless you are comparing a replacement that is similarly viable in the first place.