IMO, the window for successfully embossing the almost-cured Bondo is too short. I''d suggest a different approach.
The guys who make the embossing rolls for garage door panels (Roehlen and Stamco) just engrave the woodgrain pattern (in reverse) on a pair of emossing cylinders. It's mostly acid-engraved through a wax blanket now, but these rolls all used to be hand-engraved.
You might try just smoothing a coat of Bondo over the depression, let it set up, and then use a sharp set of woodworking chisels, V-gouges, and a rifller file to "carry the grain lines " thru the patch. Shouldn't be too difficult to get the "can't see it from my house" finish you're looking for. Study the surrounding grain lines, you'll see they vary in width, are interrupted, variable depth, etc. (you might even choose to make the one or more of the patches "knots" and feather them into the surrounding grain.)
It would be pretty easy to practice this technique. Drill or whack a golf ball-sized hole in a piece of textured OSB or cementitious siding, fill it with bondo and start engraving to match the grain lines. (might need to leave it just a tiny bit high to give you room to work with) Bondo is relatively soft, so you should get pretty good results with just hand pressure; you're not talking about doing a very large area.
Good luck.