NSS is totally separate from any DTCC issues. NSS is performed by MMs and MMs only. Retail cannot NSS. They can short, but they cannot naked short.
T4T means every trade is backed with a physical certificate, hence the large fees.
Manipulation will only be proportionately reduced by the amount of people able to manipulate. Wherever in-house clearing exists, nothing changes; buying, selling, nor shorting changes.