This is fixed in MLCD 2.3.1cs1 available through Digidesign Tech Support.
If you need to know more, there are two issues with MLCD 2.3:
First, MasterList CD 2.3 was designed to be compatible with the Yamaha CDR 8424S having a firmware version 1.0g, and for some reason the newer firmware version causes MasterList CD 2.3 to read the CDR 8424S firmware version of 1.0j as a firmware 1.08, this in turn triggers the CDR 100 message and copy flag necessity.
Second, the actual warning message and the inability to write to CDR-100s without copy flags were added to MLCD back in version 1.2 for the following reasons (from Abase # 241):
"Yamaha Japan informed us that a click (noise burst) could be written at the end of ANY track whose copy prohibit flag is set to OFF, if the CDR-100 has firmware versions 1.07 or 1.08.
Users should ensure that all tracks in the MasterList have the Copy Prohibit flag set to ON. This fix has been proven to work when tested in-house.
Version 2.3.1cs1 of MLCD will enforce the Copy Prohibit flag of each track to be set to ON, when using the CDR-100 with firmware versions 1.07 and 1.08."