I believe there has been no change to the implementation of seismic anchor motion between CAESAR II V5.20 & V5.30; the program would not calculate a strain for a single spectrum (everything strains together) and will calculate strain, if none entered, where two or more spectra are entered in a single direction.
CAESAR II does not apply a different allowable limit for these strains.
Yes, if you envelop all floors into a single shock spectrum, you will not automatically consider the strain portion of the load. This is also true if you model the building steel in CAESAR II, those strains cannot be isolated.