The platform tag is a good idea.
A possible solution could be to expand the <Platform/> tag in the manifest.xml file to target specific bit versions, so the tool could be loaded in one version and the error is omitted in the other. With proper file naming an author could make x86 or x64 specific versions and simply allow installing both at once then.
An error should not be omitted at all unless one tries to install a bit-specific version during that moment, but once installed, it should not be executed and listed. But i'm not sure if packed binaries are scannable.