Admittedly people with limited disk space probably should be isntalling a different distro, but if Sabayon is to continue to be a distro that offers a large amount of software, there is perceivable benefit in being able to choose what of it you want to install. And given that the disc is already struggling for space, it's difficult to find room for more than one disc image on it.
However, it indeed would be nice if the core install (or equivalent) could be done in such a fashion, and all the additional stuff is added onto this core item. I don't know how possible this is. i agree with you however that the 1st is more desirable than the second, if only just for its simplicity.