I'm not going to link to it, but someone made a 3rd party program that essentially puts stuff like world boss timers, gathering nodes, dulfy, a checklist system for materials, etc all into one overlay program. Needless to say I don't like it. May as well not even play the game at that point.
All it does is put a half-transparent browser window with direct links to
http://gw2timer.com/ over your game, no different than if you play windowed mode with the game snapped to the right and the timer to the left.
It doesn't play the game for you, it does nothing that a /wiki command doesn't already basically do (the wiki even has boss timers).
I think you may be overthinking the overlay. This is no different than having the wiki and timer sites open in the Steam overlay or xfire, or overwolf or whatever. Besides, if someone is going to run the World Boss train non stop for several hours, they were going to do it anyway, overlay or not. The one you're talking about isn't even the first overlay to do this, there have been several. Same for nodes and dungeon run checklists.
And let's face it, the boss timers *should* already be in the game in some form, be it an in-game calendar like WoW has, or whatever. The moment they officiated the schedule of bosses, it became a part of the game to know when they spawn, so there should have been an in-game schedule added.
TLDR; I don't use the overlay, but I do use the site it uses (
http://gw2timer.com/) on occasion, when I want to know which world boss spawns next, instead of asking in map chat, because the resource exists to me, why not use it. I'd guess that over half of the regular GAF players also use timer sites in some form or another, and have been for a looong time, so it's a bit weird to see issue with it all of a sudden.
If GW2 had a built-in calendar, boss schedule, notepad and let me scribble notes on the world map, I'd have no reason to go to a third party site to make up for ArenaNet's lack.