Exactly. Phase5 by not using custom logic was forced to pay far more per-board than if they had ASIC'd the parts together, to reduce the overall cost of production. That is why the VIC-20 could price-undercut the TI-99A so much, Commodore custom-made the chips, resulting in lower cost to produce. Yes, the R&D and initial cost is higher, but the end-price is far lower.
According to Laire, the licences to use the VHDL synthesis software were half a million. Plus R&D, they really would have no chance to break even, even if they used ASIC's. At the numbers they sold, the cost savings of the production would not outweight the R&D and setup costs.
The MiniMig, don't forget, uses a "custom made" single chip to replace 4 chips, which themselves were custom made to reduce the cost to produce the original multi-thousand-chip Lorraine unit. Your arguement about cost is a paper tiger, the cost of producing is nothing when compared to the cost savings by having reduced the overall number of parts in the product.
That is true when we're talking about numbers but look at the post I replied to and tell me, what would be the chances of the AmigaOne, for instance, being cheaper had it not been based on off-the-self hardware? This market does not really have the numbers to allow companies to produce and sell enough to cover the cost of custom hardware and make profit.