My Makawa yatsubusa has exactly the same type of graft. And it has only gotten worse with age. It was grafted in 2010 and I got it in 2012. It's quite a big tree now and I'm attempting to airlayer some of the branches off.
I've been thinking that this type of growth is caused by grafting a dwarf variety onto a standard maple rootstock and the standard trunk way out grows the dwarf tree.
I want to try a wire either at the very top of the standard or right at the base of the Makawa then mound up the soil around it. It would be acceptable if it were down at ground level or gone completely, but I want to get some parts off before I maybe kill the whole thing. I'll try to get a show me pic.