That part does not get called except on Windows 9x. The relevant part since Windows NT onwards is:

DllExport int
win32_rename(const char *oname, const char *newname)
{
    char szOldName[MAX_PATH+1];
    char szNewName[MAX_PATH+1];
    BOOL bResult;
    dTHX;

    /* XXX despite what the documentation says about MoveFileEx(),
     * it doesn't work under Windows95!
     */
    if (IsWinNT()) {
    DWORD dwFlags = MOVEFILE_COPY_ALLOWED;
        if (stricmp(newname, oname))
            dwFlags |= MOVEFILE_REPLACE_EXISTING;
        strcpy(szOldName, PerlDir_mapA(oname));
        bResult = MoveFileExA(szOldName,PerlDir_mapA(newname), dwFlags
+);
    if (!bResult) {
        DWORD err = GetLastError();
        switch (err) {
        case ERROR_BAD_NET_NAME:
        case ERROR_BAD_NETPATH:
        case ERROR_BAD_PATHNAME:
        case ERROR_FILE_NOT_FOUND:
        case ERROR_FILENAME_EXCED_RANGE:
        case ERROR_INVALID_DRIVE:
        case ERROR_NO_MORE_FILES:
        case ERROR_PATH_NOT_FOUND:
        errno = ENOENT;
        break;
        default:
        errno = EACCES;
        break;
        }
        return -1;
    }
    return 0;
[download]

... which is basically a straightforward call to MoveFileEx() and warrants no judgement on whether it is atomic or not.