Maybe complicated is the wrong word, convoluted perhaps? The basic plot of Out Of The Shadows is a bigger stretch of credulity than Alien Isolation's use of Amanda, but I can understand why they did it to set up this continuity. It's just that at this early stage there's a lot of, "well, I guess that could happen..." going on, a lot of raking over coals to start this new thread. They're getting away with these 'things that happened within the original films timelines' so far, but it's all dangerously close to Turk in the cryotube sometimes.
That aside, it's lovely to see Fox care enough to request a continuity, so it's a little niggle really. I'm enjoying the books, which is the important bit when all is said and done!