I’m not sure if anyone cares, but I was able to overcome the issue by adding two new configuration fields (xoffset and yoffset) and then altering the completion-api.js tiddler to use those fields. I can then enter in the necessary values to position the suggestion box in the right place. Setting the values to 0 make it behave like normal.
A bit clunky, but I like this plugin so much it was worth it. Since the template has a sidebar that can be enabled or disabled a different offset value has to be put in depending on whether you have the sidebar enabled or not. I just keep it enabled all the time so it isn’t a problem.
I’m sure there is a better solution but I don’t know how to program TiddlyWiki plugins so it’s the best I could do.