I like the idea of filling that space. I think your shape is fine...but to me, without some sort of edge bead, border treatment and/or being able to flare out the cover in some way, it just won't look "finished". It will look like sheet metal screwed on to cover up the battery, vs. adding a positive appearance to the bike.
I know it's a lot more work, but perhaps consider building a mold for each side using your template and adding a little depth/dimension out of foam...then make it out of fiberglass?