I started this save in the initial public release for .400 and did chapter 2 and the start of chapter 3 in the first bug fix update. Now in the current fix version I did Royal sewers > overgrown temple > Amazon Isle > Witches Academy as the game prompted and was able to break the barrier at no point did it require me to do the pharohs temple.
EDIT: I loaded a save before completing the dusty temple and while the game correctly gives you the pyramid quest there is also nothing stopping you from just going to the royal city anyway.