A Framework is a schema ... a classification scheme ... it defines a set of categories into which various things can be sorted. It is a mechanism for simplification. For example, my Framework defines a set of categories for models, primitive models that are relevant for describing a complex object like an Enterprise. A Reference Model, on the other hand, is a model, by definition, an instance of some specific kind of model.
Because models are applications of classification theory, models are technically classifications but they tend to be relevant to a specific situation. A reference model tends to be an 'industry-standard,' generic representation for some specific industry. Reference models tend to be at a fairly high level of detail to accommodate all the models of their type for Enterprises within the industry.
The reference models that I have run across tend to be composite models (because that is where we have been for the last 50 years), with either a strong process orientation or a strong technology orientation. The reference model is an instance of a model, not a classification of models. It is conceivable that you could have a (primitive) reference model for every Cell of my Framework for every industry.
I would say the intent of a matrix is to depict relationships, not classifications. For example, you could express a relationship between a Process (Row 1, Column 2) and a Thing (Row 1, Column 1), or between a Thing (Row 1, Column 1) and a Location (Row 1, Column 3), and so forth.