Hello all,
I wanted to close out this post with a solution, in case anyone else runs into this problem. It doesn’t seem that KML files will support what we want to do in terms of mission plans. However, we were able to use the Mission Plain-Text File Format to achieve our desired results (see here).
In case anyone else is interested in converting a .csv file with lat/lon coordinates to a .txt file that will enable a mission plan in QGC, you can find a Python script linked here to do so (see the maps pasted here). The input and output data for the maps are also attached here.
Big shoutout to @clyde for identifying this solution, and for writing the Python script! 
Zach
example_csv_ROV_coordinates.csv (2.3 KB)
data_output.txt (4.4 KB)
