I don't think we need to invoke philosophy regarding these technical terms.
If pressed, I'd tend to agree (after directing you to my escape clause: "...
almost a philosophical question..."), but it seems to depend somewhat on how the terms are being applied.
Mitochondrial genomes behave much differently than the genome proper, so a distinction is made in the terminology. Similarly, plasmids in a bacterium behave much differently than the bacterial genome, so a technical distinction is made.
As I mentioned above, it's important in a discussion about "altruistic behavior" to recognize what it is that is doing the 'behaving'. This is somewhat problematic, because our ideas about 'behavior' intuitively default to our first-hand knowledge about the macro-structures we refer to as "individual organisms" interacting with their environments. Frogs hop, bees sting, donkeys bray, playful children roll down grassy hills.
If we examine such behaviors in the context of their consequences for whole organisms, the math is going to work out differently than if we view them as composites of micro-behaviors at lower levels of structure (individual cells, or individual genes), and I think we risk importing some dubious conceptual baggage if we assume that 'behavior' can be regarded as equally meaningful at all levels -- when child rolls down a hill, there's a lot more going on than when a rock rolls down the same hill, even though the latter might be described as "behavior" on the part of the rock. When we speak about the "behavior" of a genome then, (or of a cell, or of a gene) we should remember that these are like rocks rolling down hills (it's especially important to remember that, because no matter where the discussion goes, it's going to be conducted in a language that is absolutely filthy with teleological assumptions).
With this caveat in mind, we could say that biological entities like cells or organelles have
interests, and that mitochondria, and plasmids, have some interests in common with the cells that contain them, some interests which are independent of those of the cells, and perhaps some that are in conflict with them. To the extent that genomes
behave, they do so by proxy; their
behavior consists of influencing the behavior of the cell (and idea which can also be extended another level down, to that of the individual gene).