ADFS 3.0/4.0 jw token and SAML with federation

Two organizations connected by ADFS 3.0 and 4.0. One of relaying party trust needs jwt (jw token). For local Active Directory based claim provider it is working perfectly but through federation no. ADFS 3.0 (4.0 probably also) can't do the translation of token from SAML to JWT and relaying party trust receiving SAML despite configuration of JWtoken for this party trust.

Of course - it can. The main requirement is WSFederation for ProtocolDefinition in properties of Relying Party Trust and of course JWToken property set to true (by default it is equal false).