Omnis can have crazy configurations without much in the way of an explanation, because you can change them so quickly. It isn't expected to be permanent in any way, so it really doesn't matter what they're carrying beyond the immediate needs of the mission.
I think the most likely reason for such a configuration would be that each Cluster carries a certain number of spare parts, but not enough to give each mech in the unit every optimal configuration. You go in asking for your normal weapons loadout, and the techs are like "I'm sorry, but the Star Colonel decided he wanted us to mount eight PPCs on his Daishi today. We have... (looks through inventory list) a Gauss Rifle, if you want that. And some medium lasers. And some SRMs. How does that sound?"
As mechs suffer damage, and your supply of spares runs low, some mechs are going to end up with sub-optimal configurations. In fact I think it would be strange if they didn't have some head-scratchers. The fact that the Inner Sphere identifies this particular setup as a recurring pattern (enough to call it "alternate B") may mean that it served some specific battlefield role, or that it wasn't that uncommon to start seeing shortages of PPCs and large pulse lasers.