Inkscape sets the SVG version of the document to 1.1 instead of 1.2, but still uses the current text.
A simple solution for you is to edit your svg document and change the SVG version attribute to 1.2. Inkscape will not change it to 1.1 and will do an excellent job with the version 1.2 specifier.
Batik will then be happy to provide most of the functionality, however, you will also encounter another Inkscape error if you make significant use of any of the text attributes in the stream root created by Inkscape. It sets the background color for the selected foreground color for the text, which means that if you set the text color to red in Inkscape, when the batik displays it, you will see a red square ... there is text, but its red color too, so in fact not visible. This is an Inkscape error and is clearly visible in the code for the streamRegion → rect element.
The solution is to manually edit the flowRect attributes after setting them using inkscape.
Batik also seems to work better if you use the standard svg output rather than the sksv inkscape output file.
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