The better solution, in my opinion, is to simply point out that a rest - whether long or short - is not a precisely timed thing. A short rest is at least 1 hour, so 3 hours spent resting is just a single short rest taking longer than the minimum required time, and a long rest is at least 8 hours, so 9 hours spent resting - even with a spell cast 8 hours into it - is just a single long rest taking longer than the minimum required time.
I agree with this. However, we aren't really talking about 9 hour rests.
A long rest completely refreshes you: hit points, spell slots, Ki points, whatever. When you are at maximum hit points, spell slots, ki points, whatever, then more resting (short or long) does not give you
more than your maximum hit points, spell slots, ki points, whatever. You are already
completely refreshed.
But we are not talking about a completely refreshed person resting for an hour.
As a player I know that I can spend hit dice to heal hit point loss after a short rest, which must be at least one hour. Meanwhile, my
character knows that resting for an hour lets him get his breath back and recover from bumps and bruises.
I know it. My PC knows it. Resting for an hour lets me recover lost hit points, lost spell slots, lost ki points, lost whatever. My PC does not know about game mechanics like hit points, spell slots or ki points, but he does know about injury and healing, that you can only cast so many spells before you can't cast any more and that you can only use ki abilities for so long before you can't use them any more, and that resting allows recovery of casting/ki ability.
Taking hit points as my example, it is true that after a long rest while I am at full hit points, then a 'short rest' of one hour straight after a long rest does nothing for my hit points; it is indistinguishable from a single 9 hour long rest.
However, after that long rest and regaining all my hit points, the first thing I do is cut myself while preparing one of the rabbits that the ranger caught for breakfast. I am now injured to the tune of, say, 4 points. I can heal those 4 points back, by ANY of the ways that can heal those points: by spell, Lay On Hands, Second Wind,
or even by resting an hour and spending hit dice! There is no game mechanic, nor any conceptual in-game reality, that denies the benefits of a short rest.
The same applies to spell slots. If you have used spell slots then you can regain those slots in any way the rules allow, including (for Pact Magic) resting for an hour.
If you have used slots then this is not resting. Your slots now need to be refreshed, and you can refresh them with a short rest.