The EQMOD ASCOM Driver setup secreen has the option to select an EPOCH that ASCOM based applications can then read. If every application did this then setting J2000 in EQMOD would effectively force every program connected to EQMOD to use the same EPOCH. Unfortunately not all ASCOM applications will read this parameter, or act upon it.
The setting of "None" is chosen as a default because that simply means that the user takes responsibility ensuring that all the applications they use are manually set to the same EPOCH - most folks will be doing this anyway.
It is important to understand that the EQPOCH setting itself doesn't affect EQMOD itself. EQMOD does not precess coordinates it recevies or those it reports - it doen't need to. Al tha tis requires is that application used during goto alignment use the same EPOCH as those applications(2) that subsequently command EQMOD gotos.