I think a sticking point in any discussion you have is "space"=nothing/vacuum/emptycontainer versus "space"=interstellar medium (where stars and spaceships do their business).

Every person who has responded to you has assumed you are talking about a container full of vacuum. Because that's what those words mean.

One answer to your question about a universe without particles and how to measure it is may be what happened before the Big Bang? The "universe" was a singularity about the size of a peach. However, it was full of stuff and not empty.

The other answer is what is outside our universe? e.g. you have an area of "space" with nothing in it, then you add a particle, what happens?

The answer is... nobody knows. The observable universe has always had stuff in it, so the size/distance/volume is measure by taking two of those points. Physics no longer works when you are talking about a universe without particles. There is no distance unless you are measuring how far apart two things are. There is no pressure without having a container.

Your scenario of a "universe" with nothing it but somehow it has reference points for scale 1m x 1m x 1m, that can't happen. There is no way to get a reference point.

Maybe the closest you will get is within string theory - it lets you have a "universe" without particles. At some point the universe was a mass of 1 dimensional strings vibrating (so we don't have 3 dimension like 1m x 1m x 1m anymore). One of those flipping in a weird way that lead to the formation of the first particle. That caused a chain reaction which created more and more particles that lead to the universe.