Please check if you need all table/view/stored proc definitions you currently have in the relational model data in the project. E.g. if you have 1000s of tables in there but map only a handful to entities, it's better to only check those in the meta-data retrieval wizard when obtaining meta-data from the database.
If that's not possible (e.g. you need all tables), check if you can recognize distinct models in the relational model. With 1000s of tables it's seldomly the case it's one coherent connected model of 1000s of entities. So in these cases, define multiple projects, one for each distinct model.
Our file is an xml file and we designed it to have only the information present that's needed, once, so there's no real redundant info in there. We haven't experimented with include files (also because that's error prone), as we never had the request to add it before (we do have customers with project files with over 10K entities)
Btw, I've never heard azure devops has a maximum file size, interesting.