Boot Disk? Self Booting Disks?

Hi, a friend of mine recently got Capcom Vs SNK on a burned CD, and it will run on the DC with out modding.. (his isnt modded) I was just wondering something... will these CDs work on Modded DCs? I read in the FAQ that it works on "ALL UNMODDED DCs"... does that mean that modded DCs will not run them?