Sorry for the delay in replying.
Unfortunately we have not tested CJT Pro with the Avada theme from CodeCanyon, so we cannot comment on that. We can say that CJT Pro and CJT Free have both worked nicely with many themes we have tested, and nobody has reported any major issues with the themes they are using. I know there are a lot of new themes are using the new parallax scrolling design so it would be interesting to know how well CJT works in regard to those. Apart from themes, the only real issues occur with security plugins, although we have workaround patches for those.
All the best.