I work at a top 10 EMR on the interface engine team. Messages between products require a lot of custom work to align message types and IDs, establishing a compendium of identifiers for external labs and identifiers, but it's not uncommon.
Yeah, but I can't take my data from Epic and move it all into Cerner via HL7, no matter what.
What we need are government standards for data at rest, similar to DICOM, for other data - and tied to Medicare reimbursement. Literally some functionary at CMS could write that rule and patients would be better off.