I see a lot of people asking the question: "So if Beamdog didn't alter the story or the gameplay of Planescape: Torment, what did they work on for the EE?". A couple of notes in that regard.
First, PST used a very unique version of the Infinity Engine. Its codebase branched off even before BG1 was released, meaning that a lot of underlying systems were radically different from those present in BG2, IWD and by extension, our EE version of the engine. In particular, the PST spell system is nothing like the systems seen in the other IE games. It took us literally months of day and night effort just to get the spells to work properly in our version of the engine, especially given the fact that they were programmed solely for the 640x480 resolution. On top of all that, the PST spell system had a number of hardcoded features such as making specific spells function differently on certain planes (try casting Heal on Carceri or Baator and see how that turns out) so we had to painstakingly reconstruct them using the original source code and design documents.
Next, we had to rebuild the UI from scratch since it too was very different from what the other IE games used. Reconstructing all aspects of the UI for a native 4K resolution while retaining the original look and feel was a big challenge. We consulted Tim Donley (the original Lead Artist) and Eric Campanella (the original 3D modeler) to ensure that the style and tone of our UI remained faithful to the original game. In addition, we had Chris Avellone review and approve every single UI screen before it became final. The code for the PST UI was also very different from what the other IE games used (i.e. animated portraits that change as party members get hurt) so making that work required quite a bit of effort as well.
Lastly, the scripting language that PST used is fairly different from that of the other IE games. Meaning that we had to implement all of the PST-specific engine functionality related to NPC AI behavior into our engine and then test it thoroughly to ensure that nothing unintentionally broke due to the vast differences in the codebase. To make sure that everything went right, we had QA repeatedly test and re-test every single quest, item, spell and area in the game. In the end, I instructed QA to do side-by-side playthroughs comparing the original PST to PST:EE to ensure that no unintentional changes were made. There's a lot more that we did beyond what was mentioned here, but this should give you a rough idea of the PST:EE development process.
TL;DR
The codebase of the original PST was vastly different compared to the other IE games. We couldn't just take the story of PST and slap it into the SoD engine, it took us months and months of hard work to get everything working properly.