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These cli parameters were designed indeed to be used before loading the config, one of the aims was that the loaded modules could be useful for processing the input for config file.
When a module is loaded, a define is set for it, like MOD_corex, I haven't checked the code if it also done for the cli option, but you can try to add to your config:
#!ifndef MOD_corex
loadmodule "corex.so"
#!endif
You can leverage further -A ... to control what modparams are set in config.
For future, a variant would be to extend load module with a new option like o to skip loading if the module was already loaded.
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