I ran into the same problem when coding the MathQuill answers and toolbar, and ended up using a few globals. In fact the pull request that stems from this discussion utilizes one of them. The answerQuills object that stores all of the MathQuill answer boxes for the page. I also designed a method to set separate options for each answer that uses global variables. The variable is something like MaThQuIlL_AnSwEr0001_Opts, of course with AnSwEr0001 replaced with the answer rule name. I am still trying to figure out a better way to do this, and to get a MathObject context to set the option. For example, parserRoot should set the rootsAreExponents option to be false.