Our approach to working with various data models is to use a different data model (https://www.biorxiv.org/content/early/2017/11/10/194597), and then to do a limited ETL into the other data models like Sentinel and OMOP. It is a little more work, but there are fewer incompatibilities. Most of the issues we have run into involve different definitions of a "visit" among the different data models. This is particularly true for claims data.
I believe FDA is working on a harmonization process. There is a presentation from earlier this year on the OHDSI site from Mitra Rocca. They may have more progress to share.