I find this boss' design somewhat interesting. It reminds me of butterflies and how they undergo a few stages before they turn from an ugly grub into a wonderful insect.
And as to why it's a mess made out of rocks and altars - it probably has to do with lunar creatures' inability to physically manifest themselves on the Constant's landscape unlike shadows. Alter guardian is, after all, just a stronger gestalt in terms of its "ethereal" form.
It's also a different kind of "scary" unlike most bosses, since it doesn't have any distinct features, and being purely an alien entity not just when it comes to its origins, but also its looks.