As noted in this support issue, the merge cells plugin is nulling out all but the root merged cell, including at the source data level, which can be seen by the response to getSourceData (as described in that support issue).
It seems incorrect to me for the plugin to be altering our source data in response to a request to visually merge the data. In fact, the documentation clearly states:
Cell merging happens on Handsontable’s visual layer and doesn’t affect your source data structure.
That was the perfect timing for this question, @dhaber as I was able to consult my colleague on a daily meeting today. Team agreed that the documentation is incorrect. Both methods