Merging two different Docx files may be very complicated because Headers, Styles, Charts, Comments, User Modification Traces and other special contents are saved in separate inner XML sub-files in each Docx. Thus, two Docx may have different objects having the same ids. So it would be a very huge job to list all possible objects in the two documents, give them new inner ids, and re-affect them in a single one. Probably only Ms Office can do this currently.
Nevertheless, if you know that your two documents to be merged have the same styles, and if you know you have no charts, headers and other special objects, then the merging becomes something quite easy to perform.
In this case, you only have to use a Zip reader, such as TbsZip, to open the first Docx file (which is technically a zip archive containing XML sub-files) ; then read the sub-file "word/document.xml" and extract the part which is between the tags < w:body >
and < /w:body >.
In the second Docx file, open the "word/content.xml" and insert the previous content just before the tag < /w:body >. Save the result in a new Docx file.
This can be done using TbsZip, like this :
<?php
include_once('tbszip.php');
$zip = new clsTbsZip();
// Open the first document
$zip->Open('doc1.docx');
$content1 = $zip->FileRead('word/document.xml');
$zip->Close();
// Extract the content of the first document
$p = strpos($content1, '<w:body');
if ($p===false) exit("Tag <w:body> not found in document 1.");
$p = strpos($content1, '>', $p);
$content1 = substr($content1, $p+1);
$p = strpos($content1, '</w:body>');
if ($p===false) exit("Tag </w:body> not found in document 1.");
$content1 = substr($content1, 0, $p);
// Insert into the second document
$zip->Open('doc2.docx');
$content2 = $zip->FileRead('word/document.xml');
$p = strpos($content2, '</w:body>');
if ($p===false) exit("Tag </w:body> not found in document 2.");
$content2 = substr_replace($content2, $content1, $p, 0);
$zip->FileReplace('word/document.xml', $content2, TBSZIP_STRING);
// Save the merge into a third file
$zip->Flush(TBSZIP_FILE, 'merge.docx');