Please note that VE does not recognize the template of el-wikipedia {{παραπομπές}}. I suppose someone has to define that. Thank you in advance.
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Templates need to be updated with TemplateData information in order to work properly with VE. You can find instructions at Help:TemplateData. If you need help from your community, you can check who added TD in the past to templates there.
That's the {{reflist}} template. VisualEditor does not insert a template in Insert > References list. Instead, it inserts the original wikitext code. It does this because
- the wikitext code is faster (when parsing/reading the page),
- it produces exactly the same output at most Wikipedias (so why pick the slower way to achieve this output?),
- it can update the contents as you edit (the same is not true for templates), and
- it works everywhere (not just at wikis that have such a template).
If you want to use the template, then you can use it. Just "Insert > Template" instead of "Insert > References list".