Many times this warnings are triggered by the packager, but if one ignore them, what is the purpose of the scans?

The software author should take a look if this is the case, for to change the packager's configuration (no encryption [if some algorithms in the programs are important, to protect them with through implementation, not packager ], or if the binary is small to not compress, or to adjust other params, etc), or to change of packager, or to contact with the antivirus company.