The issue you have highlighted with the AUI Tree structure also occurs for any other attribute.
Other similar requests I have seen include
COMBOBOX - having different ITEMS on each row.
STYLE - having different STYLES on each row.
Active - enabling or disabled fields on each row.
Any potential solution for these and your similar issue with COMMENT, would probably be similar to what currently occurs with setCellAttributes/setArrayAttributes
http://4js.com/online_documentation/fjs-fgl-manual-html/#c_fgl_ClassDialog_setArrayAttributes.html, whereby a separate array is maintained with the value. This potential solution has problems when you add/remove rows keeping the arrays in sync. Another potential solution would be to have something similar to IMAGECOLUMN whereby row level attributes are kept in the same array, this avoids the add/remove row complexity but would be harder to define.
Reuben