I've been able to fix the alignment issue in iOS devices as well as well as the scale issue I was having when embedding the content into Moodle (caused by the iFrame). It isn't a solution for the faint hearted as it requires changes to the storyline_compiled.js file, also note this worked in my situation and may not work in yours. It may not even be a good idea and cause issues down the line.
The changes are: (storyline_compiled.js)
Line 916: make .css("left",a) and .css("top",b) to .css("left",0) and .css("top",0)
Line 1014 &1015: change the variables that set the let and top css to "left:0px!important" and "top:0px!important"
these changes will make the content align to the top left of the browser
To fix the scale issue when embedded in an iFrame or LMS etc. The changes are: (storyline_compiled.js)
Line 1014&1013 make all top.window.innerHeight and top.window.innerWidth to window.innerHeight and window.innerWidth i.e. remove the "top"
I hope this helps someone.