Different operating systems use different file types and file systems. Does it make a difference to a virus scan which system it is being run on and what type of malware it's looking for? I ask because the way the files are archived may be different, for example Android's apk is in an archive so would a program like Windows Defender (running on Windows) know how to examine the contents?
In simple cases an AV wouldn't have a problem, for example an AV running on OS X and malware arriving as an .exe would raise a red flag but what about an infected RPM on Windows; Windows doesn't even know how to handle RPMs so would there be a point in scanning such files in hopes of not transferring it on to a Linux machine?
EDIT: I've seen some AVs with the option to scan inside archives, so this implies the AV would have to know how to correctly open the archive? Can viruses hide inside archives the AV doesn't know how to handle? If a archive is password protect (i.e. encrypted) than is there anything to AV can do?