I'm running a Pathfinder campaign set in Golarion, but since it's mostly aquatic I've had to design my own underwater region for the adventures to take place in. (The only official lore I'm aware of that might have been detailed enough is in the Ruins of Azlant adventure path, and one of my players has previously run that.)
I'm also taking the opportunity to adapt various underwater adventures I own, none of which were set in Golarion - e.g. War Rafts of Kron (Known World/Mystara), Sea Devils Trilogy (not really part of a setting) and Sunken Pyramid (Lonely Coast, kind-of) - so I had to change the lore to fit the world (and the campaign). I'm also about to start Feast of Dust, which is a Golarion adventure but I'm changing it from a desert adventure to an underwater adventure.
On the other hand, the nearby land is taken pretty much straight from the Dragon Empire Gazetteer (the city of Goka in particular), the included organisations such as the Pathfinder Society are true to the lore, and I ran the Ruby Phoenix Tournament adventure (also Golarion) pretty much as written.
So I went for "I use some of it and write the rest myself".
If I ever get the chance to run an Eberron game then I will stick much more closely to the established lore (or Keith Baker's own version of it, anyway), but even then I'll change some things to better suit my own preferences. (I'm sure if I ran through my list of proposed changes everybody here would prefer the official version!) Of course, Eberron is a special case in that key mysteries of the setting don't have an official answer anyway.