Unfortunately the walkthrough isn't perfect... The game actually has hundreds of scripts and most of them are redundant variations on the same scenario dependent on the stage of the game you're in... I think in the walkthrough some of those variations are navigated suboptimally because they are based on an iteration from an earlier release so if you're trying to follow the walkthrough perfectly it's not going to take you down an optimal path based on the final version of the game, as each segment is not revised based on subsequent releases...
The only way to really figure out what's going on is to track all the variable triggers and use them to figure out an optimal path through all the content, which most people aren't going to be able to do... Otherwise just follow the walkthrough as best as you can and accept that you're going to have to endure some redundancy in pathing. The good news is that with the version transitions there's little risk of missing salient content following the walkthrough. The bad news is you're going to have a lot of useless repetition and hold down the CTRL key.
The cool thing is if you have it set to skip only seen content, you'll stop whenever you get to a new iteration of a previously seen event, and you can use a tool like
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in combination with
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to figure out which iteration of the event you're on, find the variables triggered, and figure out their follow ups to determine the optimal path in combination with the walkthrough. All of that is utterly asinine, I know. The game is terribly designed but I thought there were enough gems in it to go through the trouble. Fortunately I personally play most games using these tools as a lot of devs have no idea what they're doing and they help me to avoid wasting time with bugs or missing content due to poorly designed gameplay loops.