Forget most of my analysis before. TWLTool seems to be using the term cid/ConsoleID interchangeably and use emmc_cid for commonly referred CID, and I was totally confused, looks like he is bruteforcing Console ID instead of EMMC CID despite the name 'brute_cid' suggests, EMMC CID looks not brute-able then for been 128 bits long.
About known bytes, he verified 16 bytes from offset 0x1e0, since the DSi NAND holds a MBR, that offset falls between the 3rd and 4th partition table entry, so I suppose this verification will still work with DSi.
In the end, it looks to me, OP's problem could be solved by porting the 3DS only brute force code to DSi, maybe @
WulfyStylez could answer why such thing is not implemented, maybe there're something I don't know made it impossible.