Production costs are slightly higher with a smaller run, but FunPub wouldn't be paying for R&D costs, so should only nave to pay for the necessary materials.
Keep in mind that regular Deluxe figures have a wholesale cost of about US$6-7 (including packaging), so it is unlikely that FunPub's figures would cost more than double that.
As for the new head, in the past they've produced their own cheap mould, which doesn't last long, and usually destroyed once used. Once the toys arrive from Hasbro, they attach their exlusive parts, and package them. The exclusive parts wouldn't cost more than a few cents each to produce.
Packaging costs for FunPub would actually take up a fair bit of their expense, as it is usually fancy, limited run, solid boxes.
Compared to the regular Deluxe cost of about US$6, I just can't see FunPub's deluxes costing more than 2-3 times that.
(They were able to give away 'free' their deluxe sized Membership toy last year which also had a new head - Heatwave - so can't cost them too much to do)