I am currently looking into solutions for the same issue you describe in your question. However, at my company RSA itself is used to sort out these merge conflicts. So my suggested solutions below will not work in full for you if you use a merge tool or editor that cannot work with canonicalized XML files. We do observe the same problems since we use Gerrit to review the code, and as you have stated in your question, the source code is not human readable and therefore impossible to review or comment on within the Gerrit UI.
The source code embedded in the XML documents with the .efx and .emx filename extensions, has been modified or canonicalized so that characters like linefeed, quotes and other have been replaced with corresponding HTML encoded sequences. Git and Gerrit expects each source code line to be terminated with a linefeed, so the result is almost infinitely long lines comprised of all source code lines in the so-called fragment concatenated, interspersed with some HTML encoding sequences.
Someone at our company has at least added a crude diff filter to git so that when you invoke 'git show', 'git diff' and other commands to view file content, the embedded source code lines are human readable. The filter is just a bunch of global search and replace statements replacing about a dozen or so HTML encoded sequences with corresponding UTF-8 characters.
To address this I believe there are basically two alternatives;
1) Add some sort of a filter to Gerrit that works pretty much like the diff filter for git mentioned above, replacing HTML encoding sequences into corresponding UTF-8 characters.
2) Add smudge and clean filters to git that when checking in the code, the source code lines are converted to UTF-8 inside a HTML comment placed adjacent to the HTML encoded line. In Gerrit it will then be possible to see source code as the author intended it making it possible review and comment as normal. On checkout the smudge filter removes the HTML comment and the source code within it leaving the .efx and .emx looking exactly like when RSA wrote the contents to disk. Although this will change the file contents and effectively double the size since the source code is repeated, the contents will remain a valid XML document that should not affect RSA even if the HTML comment should survive the smudge process.
Recently I heard that the latest version of RSA, 9.1 I believe, can be configured to leave the embedded source code in the fragment files more or less intact so that it can be reviewed and inspected in Gerrit without the need for workarounds such as those listed above. I have yet to confirm for myself if this actually works as described.