SCC, if they don't, then they are cheaper than base equipment and weapons that do go through the whole formula.
My argument (to test my position) is that if you built a hypothetical OmniMech that was all base except for...1 ton of OmniPod space, you still charge all that base equipment and weapons with the omni conversion cost modifier and the production cost modifier, but not the 1 ton omni gear (if using the SO repair rules to design a Pod).
For example, 60-ton OmniMech has 3 medium lasers on it's base (1 ton each) with 1 ton of OmniPod space left (extremely hypothetical example here). Those three medium lasers will each pay the results of the omni conversion cost modifier (1.25) and the final production cost modifier (in this case, 1.5), for a total of 75,000 C-Bills. But the medium laser, the only actual Omni-fied medium laser, only undergoes the omni conversion cost modifier. Being an Omni medium laser, it's actually cheaper than the ones installed as base (at 50,000). That doesn't seem right.
Plus the final production cost modifier serves a purpose: it represents the cost of putting everything together into one unit (a BattleMech, a wheeled support vehicle, etc.). The OmniPod, if the repair rules are used to 'design' a pod, doesn't have that cost. In other words, there is no cost to the 'Mech factory to build the complete OmniPod. That doesn't seem in the spirit of the final unit cost formula table, either.
My argument is that the rules for repair make sense for just that purpose: to omni-fy a standard weapon to replace a destroyed one within a produced OmniPod, not to produce an OmniPod itself. The rules specifically address (as I interpret them) just the salvage and repair of a Pod, but are not meant to provide the value of a complete, functional Pod. The unit they belong to is the complete OmniPod intended for a very specific battle unit.