Way to delegate command to methods in different files
Separate modules
You didn’t specify a file name for the code in the first block- is it something like builtin.js?
The code in the first block should be divisible into two files- one for command with executeBuiltInCommand and MOD_MODULES, and the other for vanish with USER_MODULES. They could be combined to a single module to replace the current file in the first block - what I presume is builtin.js.
Simplify .apply() syntax
The ES6 feature spread syntax can be used to replace calls to .apply().
For example:

if(isSubArg) await builtInCmdHelpers[args[1]].apply(null, [{channel,
args}, userstate]);


can be simplified to:
if(isSubArg) await builtInCmdHelpers[args[1]](...[{channel, args}, userstate]);

However, since there is a fixed length on that array of arguments, the method can be called directly:
if(isSubArg) await builtInCmdHelpers[args[1]]({channel, args}, userstate);