Thank you so much for a very detailed reply to my post; that helped immensely. And sorry for the late reply. I did some digging and found a paper that was referenced in the SITL+Gazebo sim forum (freefloating gazebo plugin).
https://hal.inria.fr/hal-01065812v2/document
The paper mentioned that since most values in the added mass matrix Ma and the Ca matrix are calculated empirically, they can be substantially wrong. As such, the freefloating Gazebo plugin disregards those matrices in the vehicle dynamics. I followed that paper and removed Ma and Ca matrices from the BlueROV2 Heavy model. Since then the model has been working very well.
And thank you for pointing out the motor mixing code. I am going through it and now have a reasonable understanding about how BlueROV works 
Thanks again for taking time to answer my questions!