Yep. Totally did it. I have no life, even if it took several months of on and off playing to do it. Protip; Helicopers are your best friend ever when you're doing this, specifically that tiny little one you could buy from the black market. It was the most maneuverable aircraft in the game, and if ya upgraded it all the way, you could get guns on it. Easy to find a place to land it in a settlement, pick up all the boxes, then hop in it and burn everything to the ground and flee to the next city before the military showed up. Fun times.
Do note however that it's basically impossible to get 100% without some kind of tool to scan your savegame for that one missing upgrade box or explodable thing that's nowhere near a town, settlement or road. As such, I have no shame admitting I used such a tool for the last 10% or so. I didn't break it out until all the settlements were at 100%.
And yes, it is impossible to get true 100%. It stays at 99.95 due to this one watertower that's missing from the map, but present in the completion list. Too bad they never fixed that with a patch.