Yep, in this game Eggman had two themes. This is more slower paced which is more fitting to the slower major bosses, such as Studiopolis' Major Boss, While Ruby Delusions are used for the higher paced bosses like Hydrocity's Major boss.

Also, I don't know if people have gotten this but the fact that Robotnik has two boss themes, is a possible reference to Sonic 3D Blast where the Genesis version had two boss themes for Eggman.