man tune2fs tells you how to set parameters. In your case,
tune2fs -O 64bit,meatdata_csum /dev/DRIVE.
However:
I doubt that enabling checksums for metadata will make your filesystem faster. The 64bit option allows your filesystem to be larger than 4 billion (2^32) blocks. I also doubt that this has anything to do with speed.
What do you mean by "direct backup"? It can't be a bit-by-bit backup, otherwise the filesystem features would be identical. Perhaps the difference is caused by the unimportant things you allude to, or by factors like fragmentation, hardware differences, number of bad blocks, ...