The QO count against the Cap. That is why RFA are the last player to be signed in NBA FA because teams look to use up any remaining cap before resigning their RFA. The only way the Spurs would lose this leverage if Green or Mills signed an offer sheet from another team. At that point, that number counts against the tendering team's Cap.
But if Green and Mills just sit tight and just resign with the Spurs, the Spurs can just resign them without using any of their BAE or MLE. The Spurs will have the Full amounts for Two Year Exception and Mid level Exception.
http://www.shamsports.com/content/pa...exceptions.jsp
Yes, reading up this it looks like the NBA made it to where these count against any remaining Cap Space.
So, the Spurs more than likely with have to trade Joseph, Blair, and Neal for a trade exception to sign both Lorbek and Diaw.
Spurs have 1mil trade exception now that can be used this FA. But they could make a trade with the Raptors, Nets, Magic, etc. for another 2mil+. which probably why they didn't want another 1st round pick but are looking to clear cap space and get some back with a Trade exception.