Just as a reference to myself and others who might encounter the same, my problem was eventually resolved after we pinpointed our problem to a third party SDK. Their investigation upon our request turns out, according to their description, to be: Swift ABI (application binary interface) has changed in version 4.2, thus causing incompatibility of the SDK.
After they modified their SDK our project compiled correctly in Xcode 10 seed and official release with both Legacy Build System, and New Build System's Incremental (default) compilation mode.
So Xcode 10 itself is fine, the only complaint is the error message is not informative enough about what's exactly wrong.