It sounds like you are talking about mentions or linked highlights. It isn’t currently possible to create queries on the referenced entities.
The main reason for this is that mentions and linked highlights can refer to any possible entity type (any database) and it is challenging to devise a technical solution to accommodate all possibilities.
i.e. for your example, the Customer field exists on the referenced entity if the reference is a Discovery Call, but not if the reference is to some other db.
The good news though is that we will roll out some features this year which will absolutely solve this problem (basically by allowing a user to specify/limit the dbs which can be used as source & target for a reference).