If I were to speculate, it would have something to do with population centers in VT and NH, with the gap between the left and right clusters representing the Connecticut River. Vermont considered itself to be a part of NH, but NY had other things to say about that. This is only speculation. I'd rather have something closer to a primary source.
Well for one thing, that's not the flag of the Vermont Republic. Or at least, we have no particular reason to think it is. We don't know if Vermont even had a flag before 1791, but if it did then no description of it has survived.
The green flag you posted is known as the "Stark Flag", after General John Stark. One of Stark's granddaughters produced some remnants of the flag in 1877 and claimed that he had flown it at the Battle of Bennington one hundred years earlier. The Green Mountain Boys also fought at that battle, and since the flag has a green silk field it's become associated with them, and by extension Vermont. But Stark was with the New Hampshire militia, not Vermont.
Also, the Stark flag didn't look exactly like the reproduction you posted. Most of the flag was cut apart for souvenirs in the century following the battle, but the top left corner is still in tact, and the actual star arrangement doesn't have that prominent gap between left and right. (Another surviving fragment suggests that the green field had some kind of central decoration on it.)
We obviously have no way of knowing what the person who sewed this particular militia flag was thinking, but there was probably no special meaning associated with it. Random star arrangements like that were common during the period. It definitely wouldn't have had a Vermont-specific meaning in any case.
