Like DA, BT have Castellans for fighting companies, marshals leading crusades, and Helbrecht being the high marshal. Also, be happy that your opponent is sinking huge points into those units. It's less stuff for you to deal with.
As for having a second master most likely refers to someone who is the master of something (Fleet, Forge, etc) and may not have their own position. For example, in the smurf omnibus Uriel is Master of the Fleet because he is captain of the 4th, but he chose to give the title away to Tiberius IIRC who would be one of the "masters of the chapter" even though he is an admiral of some type.
Now the most probable explanation is that chapter A and chapter B are fighting together, and it is not uncommon for the leaders of multiple chapters to fight together (Armageddon conflicts).
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