I advised sticking to the stations of canon, firstly because it's not Grand Order without those things occurring, it's just a different story that uses some of the setting, and secondly and most importantly because James hasn't handled the various changes they've made thus far very well and sticking to them would ease various problems in writing such an expansive story.
You know people call it fanfiction for a reason right? This isn't meant to be Fate Grand Order the video game, this is the fanfiction crossover called Hereafter. This is a fanfiction written using elements of the grand order setting and the setting of worm. I'd just like to reiterate that the moment Gudao, Gudako, and Taylor Hebert where shown to be masters it should've been a clear sign that yes, this is going to be very different than the game.
For as much as things were supposed to happen in the game a lot of stuff just isn't written that well. Also just because it's needed in the game doesn't mean it's needed here. It's really not yours or anybody's place to tell James what they have to do. While commentary, criticism, and general reader feedback is great for an author this isn't our, the readers, story to write. This is James D. Fawkes story at the end of the day. What he has to write is for him and only him to decide in the end.
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