Of course there is a lot of complicated stuff about who is moving and how fast, but at the end of it all, it seems we cannot say that there is an absolute distance between any two objects any more than we can attribute absolution motion to anything.
You are correct it is the underpinnings of SR/QM all you can ever do is give the relative motion and distance to your reference frame. Later you may find your reference frame is actually moving or subject to gravity (or worse, we will get to that) and so the measurements are only relative to you and at that particular moment in time. The measurement may be useful for a period of time and a volume of space but there is no way to generalize how long or how far.
If that is correct, the next question must be: Is there any scenario in which two objects that are seen as being separated in space in one RF can be seen as contiguous in another?
Nope there isn't any, look at the formulation of spacetime, you have a different time at every point in space that is what it says and you write it's coordinates [x, y, z, t]. All you can ever do is at some point in time have areas of space that are approximately the same enough to do some measurements that might make sense to you locally. Quantum mechanics goes further and says each of those points is evolving over time in a state of superposition.
So lets push you a bit more Bill S, and deal with superposition which extensions often gets described as weird and spooky but is actually neither. You need to understand why superposition exists and to do that you need to start with it's general description
https://en.wikipedia.org/wiki/Superposition_principleNewton and classic physics know this thing as cause and effect. The problem with classical physics is it gives no idea why such a thing should be connected you just have to accept it.
Superposition is the mechanism that QM says is responsible for why cause and effect are connected. It is telling you the universe as far as we can tell is a linear system and we can write the relationship as Schrödinger's wave equation and connect everything thru descriptions of energy or information.
The superposition which connects cause and effect, because it is a wave can have some strange properties like entanglement. A lot of science media tend to suggest that entanglement is defying cause and effect when it's actually the reverse it is showing just how connected they. The problem is the connection is not in the normal space dimensions of classical physics.
So the lesson here is no you can not rely on any measurement as that measurement is in superposition with the universe. Measurements are useful locally in so much as they allow you to interact with the universe and effect outcomes. Those measurements however are distinctly local and distinctly transient to a point in time.
That realization lead to an experimental test called the Quantum Eraser experiment (
https://en.wikipedia.org/wiki/Quantum_eraser_experiment).
The experiment throws up how heavily cause and effect are connected that a change in the superposition ignores time ordering of measurement events. Yes some event in the future can make your measurement wrong it's just rare for us to see it.
Now if you got the full connection you should be able to realize you can play with the time evolution by continually measuring which is called the Quantum zeno effect. Topically this had a writeup last week (
http://phys.org/news/2015-10-zeno-effect-verifiedatoms-wont.html)
There is nothing new in any of this it has been known by anyone who cared to look at the science for 85 years. Special relativity and QM are different frameworks to describe the same thing a universe in which there are no absolutes and space and time are connected via cause and effect.
So there you have your answer that no measurement can ever be absolute, they can only ever be relative and only guaranteed to be correct at the moment you took it
Perhaps you need to consider what you are doing when you measure something .. try thinking in QFT terms.