In MC (in DirectShow in general), if you select a particular filter for a file type, that filter gets high priority. Therefore if the filter is usable, it will be used. If the filter is not usable, another filter will be used.
I can not reproduce the behavior your described. If I select AC3Filter for AC3 files, AC3Filter will be used. If I select FFDShow Audio decoder, then FFDShow Audio Decoder is used. If I do not select either filter, then AC3Filter or FFDShow Audio Decoder is used depending on their merit - AC3Filter if "Prefer AC3Filter" is checked on AC3Filter configuration, FFDShow if "Prefer other decoder" is checked on AC3Filter configuration.