Disclaimer: I only defeated 8 of the 9 bonus bosses in question.

 

There are some bonus bosses that are available on all difficulties, even solo mode, albeit with highly variable difficulty to unlock, some of which are available unconditionally (Iokath chain, especially Nathema, which is run pretty much systematically in those few occasions I actually ran Nathema) others who only require a little extra effort to unlock (such as False Emp, Foundry) and others still that require a dedicated effort to unlock (such as Ilum, Taral V).

 

And there are those bonus bosses that are only available in MM, and not in VM (and not in SM either, whenever applicable). Here is the list of the FPs:

 

- Hammer Station

- Athiss

- Cademimu

- Mando Raiders

- Incursion on Korriban

- Assault on Tython

- Depths of Manaan

- Legacy of the Rakata

- Battle of Rishi

 

I get that the first six are often skipped (on Cademimu, however, running it usually means the team has neither Salvage nor Slicing) despite them being mechanically manageable for teams capable of clearing the FPs in question. And I also understand that bonus bosses in Manaan, Rakata and Rishi are much less straightforward mechanically than the first six.

 

The question becomes: why is it that bonus bosses in these nine FPs mentioned above are only available in MM, and not for all difficulties?

The first 4 only received a hard mode in 2.0, which also added the bonus bosses. The rest are all in the Forged Alliances/SoR chain, so I guess it was just the decision of the developers at the time.