During review of JDK-8311302 (implementation of JEP 493) it was pointed out that we should handle the case of JDK modules being patched better. After JDK-8311302 there is this code in JRTArchive, specifically in JRTArchiveFile.toEntry() which handles this case:

                            try {
                                return Files.size(archive.getPath().resolve(resPath));
                            } catch (NoSuchFileException file) {
                                // This indicates that we don't find the class in the
                                // modules image using the JRT FS provider. Yet, we find
                                // the class using the system module finder. Therefore,
                                // we have a patched module. Mention that module patching
                                // is not supported.
                                throw new RuntimeImageLinkException(file.getFile(), PATCH_MODULE);
                            }

It might make more sense to detect JDK module patches earlier and abort the link for links from the run-time image.