Now that we have permalinks, page links should be stored like this (I think option 1 is better);
<a href="page://Eesj89FnbMzMMvs0">Other Page</a> // 
<a href="https://yoursite.com/@/page/Eesj89FnbMzMMvs0">Other Page</a> // 
However, for the frontend, I think the output should look like this:
<a href="https://yoursite.com/lorem/ipsum/other-page">Other Page</a>
This means that the text stored in the .txt files will have to be converted somehow, which could be a bit difficult and will also be a small performance drawback.