I don't think a couple of 1/4" holes will be a problem. However if it starts to look like termites took over . . .
Are there any holes left over from the manufacture? If they are in the wrong location, perhaps a hook can be bolted to your platform, and hold it in place.
My other thought is clamping from top of the frame to bottom of the frame, so you might have a 7/8" thick unistrut under the battery platform, and clamp to that? That would avoid any holes into the frame.
If it is tempered steel, it will be difficult to drill through it. Use plenty of oil, and start out with a smaller pilot hole, say 1/8"?
You will find that the pair of 6 volt batteries will last much longer than the 12 volt they replaced.
Good luck!
Fred.