The use of the .sys.ini language files is a new feature in Joomla! 1.6. As written in the Joomla! 1.6 Documentation these .sys.ini files are used for extension description translations on the install and update screens.
If you check out the .sys.ini language file of a default template, such as en-GB.tpl_beez_20.sys.ini for the Beez 2 template, you will see, that the template positions are also added to this language file.
These position translations are used in the second column of the template positions modal opened by clicking the ‘Select position’ button next to the ‘Position’ field in the ‘Details’ section of a module edit screen.
It would be great if the JA T3 Blank template had such .sys.ini support, not to speak of the JA T3 and JA Typo plugins.