While a compartment representation is valid for searches (GET), is it incorrect to use the compartment based representation for POST/PUT interactions.
For instance -
GET [base]/Patient/[id]/Condition - this is the usage pattern mentioned for compartments (http://www.hl7.org/fhir/compartmentdefinition.html#use)
however, is this also correct -
POST/PUT [base]/Patient/[id]/Condition
That's not presently supported. Feel free to submit a change request if you'd like for such a feature to be considered. (It's actually a good idea to submit a change request for clarification either way.)