Space ("bigger") and time are interrelated concepts (same damn thing/Minkowski vector) - if you have less time in an area (i.e. due to a gravity well, like Earth's) you can equally view it as more space.The metric in a gravity well like Earth's is not the Minkowski metric, so you can't interpret gravitational time dilation (which is what you are referring to by "less time" in a gravity well) the same way you would interpret time dilation in special relativity. The simplest way to see this is to observe that gravitational time dilation is present even when everything is at rest relative to each other, whereas time dilation in special relativity requires relative motion.
the "volume" of "space" measured from within Earth's gravity well out to a fixed distance (say EML-1, for the sake of argument), differs to the same volume as measured from outside of the gravity well.
This is not correct as you state it. What is correct is that the volume you measure depends on your state of motion: the volume of space you will measure out to a certain radius from the Earth will be larger if you are at rest relative to the Earth than if you are free-falling inward towards the Earth. But two observers both in the same state of motion will measure the same volume of space out to a fixed radius from the Earth, regardless of their location relative to Earth's gravity well.
If cosmic voids have less space in them
This isn't consistent with their hypothesis; their hypothesis is that the voids have more space in them, not less. So you can't combine this with anything in their model to get a valid answer; you're starting with inconsistent premises.
(i.e. more time)
Less space does not mean more time; see above.
(if you don't have any matter-energy in a volume, then what "keeps" time?)
The voids don't have zero matter-energy; they just have a lot less than other parts of the universe (at least, according to our best current observations.) That said, spacetime itself can "keep time" even if there is no matter-energy present in a particular location.