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You have to make a basic assumption in your ruler case: the two matter particles must not be interacting with each other or the ruler (or anything else). In that case, there's nothing holding them together
This reminds me of the demonstration used so often to illustrate the universe's expansion: Points marked on a balloon move apart as it's inflated. If a ruler was drawn on the balloon, we'd see that the scale expands also. Thus, distances among galaxies as indicated by the ruler would remain unchanged. This screws up the expanding-universe explanation (i.e., it raises the question of how we're managing to measure it), but illustrates pretty well why I'm having trouble understanding why space expansion doesn't affect distances among atoms, among mesons, of electrons from their nuclei, etc., and how we could detect it if it were happening. Space is space, whether we're talking about "outer" space or space separating particles.
...A "better" way to think of the balloon model is to think of your ruler as a small string sitting on the balloon. If you blow up the balloon, it gets bigger, but the string doesn't really get stretched. If you chop the string into pieces, these are now acting like noninteracting particles in space, and those pieces do get moved apart as the balloon expands.