Make room to show more related questions
For many questions, the "Related" items are just a small selection from a much longer list. Showing items in both lists, "Linked" and "Related", means other related items have to be omitted. This means useful information is being lost.
Since the two links are right next to each other on the screen, there is no benefit to the duplication, only a missed opportunity to show more relevant information.
Although this meta question is a few years old, I can confirm that this duplication still happens today. It is particularly wasteful in cases where a number of different questions are shown in the "Linked" section, with their duplicates taking up a significant proportion of the "Related" section.
Note that a very similar question was raised as a bug in 2010, and closed as status-by-design in 2011, and the redundancy tag was removed in 2012. The fact that this behaviour was intentional doesn't seem like a good reason to avoid improving it, and the redundancy could even be avoided by having a list for "Linked and Related", as suggested in a late answer there. This would save space any time there were more than 1 duplicate, and improve clarity even where the space is the same.