Is there a way to instruct the CodeWarrior IDE to use relative paths instead of absolute ones to store the project file location in a workspace?

Yes. When you create the project in the default location which is the workspace directory, no .location file gets created and you just have to zip the project and the workspace. Before you create the zip file make sure that you remove the following:

• The project build directory since there will be absolute paths in the .mk and .args files.
• The workspace .metadata\.plugins\.org.eclipse.ltk.core.refactoring directory.
• The workspace .metadata\.plugins\org.eclipse.ltk.core.resources\.history directory.
• The .PDOM files from .metadata\.plugins\org.eclipse.cdt.core directory.