Release : 12.0
Component : CA MAINFRAME APPLICATION TUNER
It is recommended to use TRCUST or MSM to perform MAT custonizations.
You are correct in everything you've stated in this case. Your decision to have the CICS team redo their work using TRCUST is the proper one.
The members of CEESOPTN contain the default values for MAT parameters as they were released by Broadcom.
When you customize MAT, you should use either TRCUST or Mainframe Software Manager, as those are the supported customization mechanisms. Either of these tools will place modified parameter members in the UTRPARM library, which is then concatenated in the MAT Server JCL ahead of CEESOPTN in the TUNPARM DD statement.
The benefits of this approach are that the "human factor" is largely lessened because the parameter syntax is generated programatically, which means it will be correct (that is, no typos). Of course, you have to provide the necessary data values, and there could be a typo there, but that is unavoidable.
It is also easier to back out a change, either temporarily or permanently, when you have the unaltered parameter members in CEESOPTN.
Lastly, changes made to any CEES* library outside of SMP can cause problems when maintenance is applied. At the very least, your changes would be lost. The worst case is that maintenance would not apply due to differences between what SMP knows and what is actually in the library.