whether an ATPL holds embedded spa-ir privileges?
No it doesn't. Although according to JAR-FCL amendment 4 it is possible to maintain (ie revalidate, but not renew) a SPA-IR based on having a current MPA-IR and meeting certain recency requirements.
You might be confused with the former UK national CPL/ATPL, which had (or have, if you still hold one) 'embedded' IMC rating privileges.