Shame on me. The TeXML processor had a bug in the core functionality.
Consider the following XML:
<para> Paragraph starts ... ... and ends. </para>
One can try to translate it to TeX this way:
Paragraph starts ... ... and ends. \\pre
But this conversion is invalid. In TeX, a blank line creates a paragraph break. In the example above, we have two paragraphs instead of one.
TeXML comments out blank lines to avoid paragraph breaks:
Paragraph starts ... % ... and ends. \\pre
The bug was in understanding what is a blank line. The blank line in TeX is not just the empty line. The blank line is a line which consists of zero or more space characters. Now the bug is fixed.