The newer version of the project wizard format, used by Anjuta 2.31 and greater, supports the standard xml:lang attribute. So the translation can be merged in the .wiz file considering it as an xml file and using standard tools. The attributes having a name starting with '_' are considered as translatable.
The translation tools (intltool-merge) has to recognized the .wiz as an .xml file before being preprocessed by autogen. This adds additional constraints when writing the .wiz file, in particular you have to take care of quoting in attribute values. In addition, you need to have the project-template root node. So your template will not be compatible with older version of Anjuta.