You mention using siteliner tool which checks only for internal duplciate content, however I will also talk about external duplication of content.
External Duplicate Content
Copy a paragraph or two of the content that is worrying you and
paste that into a Google search.
Do you see your site coming up at the top of the search result? If not and there are other sites above you with the same content, then yes you have issues with external duplciate content and Google is not seeing your page as the original source.
This isn't necessarily penalising your entire site, however its penalising your site in the sense that pages that have externally duplicated content wont be ranking as well as if they had unique content on.
Internal Duplicate Content
Copy a paragraph or two of the content that is worrying you and
paste that into a Google search using this search operator
site:exmaple.com then type the paragraph of text here
Do you see lots of different pages coming up in the search results from your site. If yes then you may have issues with internal duplciate content.
The issue here depends on how much of content is duplicated internally. Is it wholesale sections of main content (issue), or is just some boilerplate content that appears on all pages, but the majority of content on the pages is unique (no real issue)?
Again, this isn't necessarily penalising your entire site, however its penalising your site in the sense that pages that have internally duplicated may not be ranking as well as if they had unique content on.
The main issue with large scale internal duplicate content, is that the incorrect pages may appear in the search results than what you would like to appear and/or pages may drop into Google 'omitted results' as deemed not relevant enough to rank.
So you can do some research, use the results from siteliner and search for that content in Google and see how you are ranking.
Are you not appearing at all, are rankings low, are pages ranking from your site page where you would prefer other pages to be ranking in their place, do you see some pages dropping into the omitted results, etc.
If you see any such issue, than fix as necessary.