When a Limited SRS list is configured in the general WCS settings then only the CRSs from the short list appear in the WCS 2.0.1 GetCapabilities. However, GeoServer still supports the use of any other CRS in SubsettingCRS and OutputCRS parameters. By the WCS 2.0 standard this is wrong:
"Requirement 12 crs/getCoverage-outputCrs-availableCrs:
The outputCrs parameter in a GetCoverage request, if present, shall have as its value a
CRS Identifier described in the crsSupported list delivered in the CrsMetadata
element of the Capabilities document of the server addressed."
Using a CRS that does not appear in GetCapabilities should yield OutputCrs-