You're fine :-) Apparently M5A99X-EVO-R20-ASUS-1302.CAP is not exactly 8MB, which is the size of your flash chip (W25Q64). This is just a simple sanity check flashrom uses to help prevent flashing the wrong file to your chip.
I took a quick look at a BIOS image from Asus' website and it appears that they append 2KB to their BIOS image:
007ff060 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |................|
*
00800780 50 45 49 45 2b ac f5 ff 10 00 00 00 00 00 00 00 |PEIE+...........|
00800790 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |................|
*
008007f0 e9 0d e0 ff ff 00 00 10 00 00 78 56 00 00 f0 ff |..........xV....|
00800800
Usually this junk vendors append to their BIOSes is benign, but you never really know... I recommend looking around to see if anyone else has had success flashing this board using Flashrom. I do not recommend bypassing the size check or truncating the extra 2KB unless you have a means of recovering (Backup BIOS ROM, external programmer, etc).