I think before the Finance and Felony Update, GTAO was fairly consistent with being before Story Mode. However since then, Rockstar pretty much gave a middle finger to that, and just did whatever they want. If it is current time, Merryweather should be long gone from LS. There should be some remnants of the UD Heist the Trio did. The building Lester torched is still intact.
At this point I just look at GTAO as a separate entity.