I am trying to copy some pages from the online GIMP documentation and the two files that I have uploaded are being rendered differently in Obsidian in such a way that I’m able to make Internal links in the Part I. Getting Started.md file easily, but same cannot be done in Table of Contents.md
Short answer : because neither of these two files is following a correct Markdown syntax in order to obtain the result you’re looking for.
It’s not an Obsidian issue, it’s an issue with your writing. I advise you to study the bases of Markdown syntax using something like this CommonMark dingus.
Or simply setup Obsidian so that you have the RAW source in a pane and the Preview in another pane.
Learn the basics, step by step. There are plenty of tutorials on the internet, text based or video.
Specifically, in the first one, the indented list items are below a parent list item. This is correct Markdown.
In the second one, the list items are floating without a parent list item. They are under a heading. So they are indented, causing it to be a code-block or preformatted. So no Markdown syntax is going to render properly.