Is it a commercial package? Like one from a vendor? If so, I wouldn't bother trying to convert it since it might be in a non flat format for a reason.
If it's something you built, and you have the Composer source, you need to make sure your Composer preferences are set to use the "Build flat PKGs" option. Also make sure your source isn't using any of the script formats that can't be used in a flat pkg - the only 2 that work with flat packages are 'preinstall' and 'postinstall' All the others, like postflight, preflight, InstallationCheck, VolumeCheck and others are not supported in flat packages. If any of those are present, when you build the package, Composer will prompt you if you want to build it as a bundle style package because of those scripts.
Ultimately, I wouldn't worry too much about it being zipped unless it's causing you some issues. The Jamf Pro server knows how to handle them and unzip them once it downloads to the client.
