Yup, OMEMO and Olm are bit compatible. In fact XEP-0384 went through a phase of recommending Olm as the implementation to use (grep https://xmpp.org/extensions/xep-0384.html for Olm).
(Although the bifrost bridge doesn't currently implement E2EE - and it would have to reencrypt anyway to turn the Matrix event payloads into XMPP stanzas and vice versa)
Does Matrix support OMEMO for e2e encryption?