Jiggle this wave just right and you effectively make it bigger. Its wavelength is lower, it has less energy.
That tells you something about how relativity will treat this box. Yes, the box as a whole will behave like the binding energy is just part of the mass.
Please stop bringing it up. The fact is that there
is something going on inside the box, and that there are laws of physics that tell you about the different things that can happen inside the box. We can put things in the box that have kinetic energy, or mass energy, or binding energy, and
they can be different. A microgram of uranium, a microgram of graphene, a microgram of cold 4f-excited hydrogen atoms, and a microgram of photons-trapped-in-a-hot-cavity? Yes, they all weigh a microgram. Thank you.
Saying "they all weigh a microgram" does not mean they're all the same thing.
Saying "think about jiggling the microgram and finding that it weighs a microgram" does not mean that there are no differences between the uranium and the hydrogen and the photons.
Saying "well, whatever's in the cavity, it has a wavelength, and it weighs a microgram" does not mean
we can't talk about the laws of physics that determine what goes on. There are laws of physics that we can apply inside the box---without jiggling it---that let us talk about details of this box
in addition to, but including, what it weighs. The behavior of the box-of-uranium (in contexts other than 'its mass when jiggling it') is different than the behavior of the box-of-photons.
To talk about those differences, we have to talk about
laws of physics inside the box, laws detailed enough to tell us
something other than the total mass. Please, please, please stop telling us to jiggle the box. Jiggling the box helps you measure the total mass, independent of whether it is rest mass or bouncing particles or a standing wave. I know. I don't care. That's not what we are talking about. Please stop.