I've been dabbling in Valve's Hammer for the past year but I would still prefer, after all these years, if I could use Quake3 engines's GtkRadiant. I just worked faster in GtkRadiant and could apply textures much easier. Maybe it's just "old habits die hard" but I actually can't make a 90 degree round pipe in Hammer and any interesting mesh structure anymore (e.g. round doorway) without using models, unlike in Gtk. Play around with brush vertexes in Hammer too much and things just break.
Problem comes when I want to make decent terrain that works around general brushwork in Gtk. So I think this editor helps.
For me at least and my limited experience with brush-based map editors, playing around with vertexes too much leads to gaps and "leaks" that are hard to keep track of and halt the BSP process. I've seen time-elapse videos of maps being made, including ones from
Valve, and a lot of time is spent just making brushes off brushes aligned with brushes to "set the stage" for later detailing work. It's easier, for me, to base/snap things off brush surfaces instead of using a divorced 2D grid operating somewhere in 3D space when the map brushwork gets more complex.
Although I haven't touched JED over a decade so I'm not sure if we are talking about the same things...