@chens, currently you cannot store settings like this in Handsontable’s settings. You can however put anything you’d like in DOM, as Handsontable operates on standard HTML elements.
For example, you can set attach additional data to cells using the setCellMeta method (see: http://docs.handsontable.com/Core.html#setCellMeta), and then add them to TD elements using the afterRenderer hook.
See this simplified example: http://codepen.io/js-ziggle/pen/PNRrwY
It adds data-custom attribute to cell at (1,1).
Adding it using the cellMeta ensures that the data won’t be lost after re-rendering the table.