It is two different flavours. One is about interconnecting things, and the other is what you interconnect. What TFA called modelling abstraction seems to be the primitive ideas that goes in building more complex systems (which it calls Modularity Abstraction). Something like a String is not a primitive, but rather a combination of the idea of Character and List are. Just like you can go from a disk (a pure array of bytes) to a file system (in the unix world, a tree with nodes of metadata). The primitive here are Array (existing) and Tree (target) and with them you build a modular system (The file systems) that transform ones into another.
So yes, both are abstractions, one is about identifying primitives, and the other is about combining them.