We use spring-data-neo4j and ogm, and have been using this extension successfully for several months to implement multi-tenancy on a single server instance: GitHub - meistermeier/neo4j-ogm-label-extension: Example of a cypher modification provider for Neo4j-OGM
Essentially what it does is automatically append an extra label to every node in your query. In your session config, you can specify a hard-coded tenant id or use a Supplier object to make it dynamic. It works well for most queries, although I have found a couple of cases where it does not (e.g. using the same variable name across WITH queries, or inside an apoc.do.when). Otherwise it's pretty solid, and we have had it in production for several months.
I do not believe it will work for the case you note, however. If you are mixing non-tenant nodes with tenant-specific nodes in the same query, it's not smart enough to know which to append labels and which not (afaik anyway). also note that it does not add labels to relationships, only nodes.