Each quality goal has associated support costs.  In the software world, if I use caching, encryption, and exception handling, these quality functions support improved response time, data security, and product robustness and have associated costs.

It has been said that "Quality is Free".  This doesn't mean that quality needs no investment, but rather that its ROI is much greater than 100%.  Support costs are a major part of this investment along with verification and defect removal costs. 

Since support costs are substantial, project estimates should include costs for quality goals. Quality-Aware estimation refers to the inclusion of these quality support costs.

The function point user group (IFPUG) has recognized the importance of quality support costs and estimates them along with technical requirements costs using their Software Non-functional Assessment Process (SNAP).  Information about SNAP is available in the SNAP Assessment Practices Manual (available on the web).

Since Agile's estimates focus on user stories and story points, quality goals have no influence.  Since Agile's awareness of quality goals is unpredictable, story point estimation is likely to be based on domain functionality only.