I have a vague recollection that the iPhone used to be behind the iPod Touch on memory because the Touch had two memory slots to the one in the equivalent iPhone, due to not having the same internal components. Is that still the case?
Yes, but that is irrelevant to the issue as to whether Apple will improve the cost per GB. They could get rid of the 16 GB and return to offering two models, 32 at $199 and 64 at $299.
128 GB nand modules came out earlier this year, but I doubt apple will use them right away. It took them well over a year to start using the 64 GB ones. The supply that they need probably isn't there yet.