What's the problem with the holes? But if you insist, anything beyond bondo is overkill.
Stress fracture at that point might be a problem. Sweat and water intrusion is another. Filling it with epoxy won't solve the prior, but will help the latter. I'm not quite sure it's a problem, but I'm definitely not sure it isn't. Could be a case of FUD, but perhaps not. I wouldn't recommend just drilling a hole through the frame to pass cable housing through. What could possibly go wrong?
I did a similar job for [MENTION=168558]Drillium Dude[/MENTION] awhile back on his Casati. For small holes I used silver to fill, larger ones brass. Bigger yet I used a bit of brass stock and silvered it in. Of course these were all filed and sanded flush with the rest of the tubing. The elephant int he room is the cost of repainting.
Those holes are far enough away from the chrome, no worries about heat affecting that.