In QGIS, I am trying to use the Create Grid for Indexing plugin more efficiently. I would like to know if it is possible to export a map composer extent to a layer (a layer with one rectangle polygon) in order to use it as the layer extent in the Create Grid for Indexing plugin.
It's difficult to get zoom to extent to work without gaps, as you've found. It gives "best fit" when the aspect ratios don't match.
(Tip : when messing around with extents, use CtrlB to save extents on a saved layer, that way you can always get your extent back, even after closing QGIS)
Snapping indexed grid to bounding box
If you want to create a grid over the extent of a layer:-
Make sure the layer is selected in the Layers panel first, then click on Selected Layer in the plugin. It should then build the grid inside that rectangle.
If you uncheck the option add labels outside extent that will create a plain grid.. that might make things easier in composer.
You could then use composer to expand to fit the content (needs QGIS >2.12?)