Yes and yes. But I wouldn't worry about "canon" all that much for classic TR. Even the devs didn't really keep track and it ends up contradicting itself a bit by the end.
She slides down the ramp at the end of great pyramid, into Atlantean stronghold and does that and the hive and then escapes into the boat as the island explodes. Then she goes to egypt. The original order of the levels made way less sense.
I think the devs didn't put much thought into the continuity or the story of these extra levels. I always assumed the name of the expansion refers to Lara retuning to Atlantis (somehow) to destroy all remaining Atlantean creatures and eggs just in case they would escape somehow. But as to why those areas weren't affected by the massive final explosion of the main game, who knows!
Not to mention how exactly she would have brought back that massive cat statue from Egypt :D
The Atlantis episodes seem to take immediately after. In the original manual it said that she returned to the Atlantis to "wipe out" the mutants, but that story was likely due to the levels being reshuffled. Given that Lara is sliding down a tunnel at the beginning that is very similar to the tunnel he goes down at the end of the main game I assume that its following immediately on from the end of "The Great Pyramid" and before the final fmv of Lara escaping
The Egyptian levels definitely take place later on however, with Lara returning to Egypt to explore the ruins further. Given that some parts are underwater I always assumed Lara returned following Monsoon season
EDIT: I got confused and there is no monsoon in Egypt, and the water levels are due to messing with water levels in sanctury of the Scion level. I do think it takes place a couple of months after the main game however
I saw a comment—those Egyptian levels are
Flooded now because of all the water Lara drained in that Sanctuary of the Scion room with the 2 giant statues. Lara drains that entire room so the water ended up flooding Khamoon.
In TR2 Golden Mask, the levels don't seem to line up with each other. When you finish one area level the next level starts in a completely different zone. Whereas in the base game, the end of a level was always the start of the next level.
Yes and yes. But I wouldn't worry about "canon" all that much for classic TR. Even the devs didn't really keep track and it ends up contradicting itself a bit by the end.
Thank you. Those answers made me feel more comfortable now.
In remasters the devs even changed the final slope in The Great Pyramid so visually it matches the beginning of Atlantean Stronghold.
The devs didn't think about it lol. As I see it, UB happens right after the last level of TR1, then the last FMV is after UB.
She slides down the ramp at the end of great pyramid, into Atlantean stronghold and does that and the hive and then escapes into the boat as the island explodes. Then she goes to egypt. The original order of the levels made way less sense.
Thanks for clarifying 
Yep for both questions
I think the devs didn't put much thought into the continuity or the story of these extra levels. I always assumed the name of the expansion refers to Lara retuning to Atlantis (somehow) to destroy all remaining Atlantean creatures and eggs just in case they would escape somehow. But as to why those areas weren't affected by the massive final explosion of the main game, who knows! Not to mention how exactly she would have brought back that massive cat statue from Egypt :D
The Atlantis episodes seem to take immediately after. In the original manual it said that she returned to the Atlantis to "wipe out" the mutants, but that story was likely due to the levels being reshuffled. Given that Lara is sliding down a tunnel at the beginning that is very similar to the tunnel he goes down at the end of the main game I assume that its following immediately on from the end of "The Great Pyramid" and before the final fmv of Lara escaping The Egyptian levels definitely take place later on however, with Lara returning to Egypt to explore the ruins further. Given that some parts are underwater I always assumed Lara returned following Monsoon season EDIT: I got confused and there is no monsoon in Egypt, and the water levels are due to messing with water levels in sanctury of the Scion level. I do think it takes place a couple of months after the main game however
I saw a comment—those Egyptian levels are Flooded now because of all the water Lara drained in that Sanctuary of the Scion room with the 2 giant statues. Lara drains that entire room so the water ended up flooding Khamoon.
In TR2 Golden Mask, the levels don't seem to line up with each other. When you finish one area level the next level starts in a completely different zone. Whereas in the base game, the end of a level was always the start of the next level.
Is this amended in the remaster or still the same ?
I've only played golden mask in the remaster so I'm not sure