As I have the detailed knowledge about the game and TAS, I'll try to organize information about this situation.
Improvements included in
[1837] NES Atlantis no Nazo by Sonikkustar in 02:23.11
1. 2P pause trick (found by NitroGenesis)
By pause trick, transition time in each zone become shorter, and 2P pause trick enable to omit a blank frame by using 2P start button.
However, this trick may have something to do with
emulation issues, because
Famicom 2P controller has no start button. (And this game is released in Japan only) So, whether this trick is allowed should be discussed IMO.
2. Better Acceleration in 99th zone. (found by Me)
3. Better Bomb Throwing in 99th zone. (found by Sonikkustar)
This improvement probably lost meanings due to New pause trick found by exposure.
Improvements included in this submission
New Pause trick (found by exposure)
This trick enables the closed secret door to be open at the same time Secret door appears, and is used in 93th and 99th zones.
In this game, there are two types of the secret doors.
1.Opened secret doors (11th zone and 52th zone in the TAS)
You can't see the door itself, but you warp to Next Zone when you move to the door's position. (So, suicide bombing is noting to do with warping. In 11th zone, there's no way to move you to the door's position except for suicide bombing. In 52th zone, suicide bombing is just faster. )
2.Closed secret doors (93th and 99th zones int the TAS)
You can make the Closed door appear by throwing bomb to the door's position. New Pause trick omitted this process.
Exposure and Spikestuff didn't include the improvements in the Sonikkustar's submission, so MESHUGGAH did that.