The default settings enable all DLCs you own. If you want to disable specific DLCs or enable Mods without using the launcher you will have to edit the file "dlc_load.json", usually located in "C:\Users\your_username\Documents\Paradox Interactive\Europa Universalis IV" (Windows), "~/.local/share/Paradox Interactive/Europa Universalis IV" (Linux) or "~/Documents/Paradox Interactive/Europa Universalis IV" (macOS).
To disable DLCs, add them to the "disabled_dlcs" list, to enable mods add them to the "enabled_mods" list.
"dlc_load.json" Example:
{
"disabled_dlcs":["dlc/dlc065_fredmans_midsummer_epistles/dlc065.dlc","dlc/dlc052_sabaton_soundtrack/dlc052.dlc"],
"enabled_mods":["mod/ugc_1792575623.mod"]
}