Good. That warning can be ignored. It's a (more or less personal) development branch. Please comment it in cart_intersect.hpp if you want to get rid of it. I will fix this but it is, for me, diagnostic information
Ah, that is a known problematic side-effect. That has to be fixed too but of course, if you need it today, or even somewhere this week, I cannot do that.
You can try one more thing: please define BOOST_GEOMETRY_NO_ROBUSTNESS. It will than skip all rescaling-to-integer-for-robustness code. That sounds a bit weird, because this thread was to fix that. But besides the rescaling more enhancements have been made, so it might be that your code then runs OK. However, I cannot predict that, there are also cases which really need this rescaling. So you can try how it looks.
Besides that, maybe even better, you can try to call the function "geometry::remove_spikes" on your output. It hopefully will remove all spikes which are generated.
Finally, could you also send me the WKT's of your input, for me to check that generated internal spike (as we call it)?