There isn’t a firm convention here. At the base design level, Tinderbox cleaves to original hypertext notions: links are two-way and stored outside the note’s text, i.e. not in $Text. To get a glimpse into the latter, see The XML TBX format †. You see the links in the $Text pane because the app overlays the links from the linkbase‡ onto the text. This is different from post Web-era designs that adopt the HTML approach of coding (so hard-wiring) the links into the text.
So whilst links are drawn (where drawn, e.g. maps) with a source and destination, the stored link is between two $ID values … pertinently they aren’t altered if either end moves in or between containers. Ignoring the visual style, compare Map and Hyperbolic view. The latter is drawn using links—regardless of direction—as the framework for which notes are shown: not linked, not shown.
I think the built-in footnotes having explicit back links (not to footnote, footnote to note) was likely for map users to ‘see’ a backlink. It is the case the outbound (text) links are most easily seen, and translate to HTML or Markdown, etc., export. But as shown in the meeting, Command-apostrophe ( ⌘+') or menu Note ▸ Go Back will traverse the last-used link backwards.
A recent addition to aTbRef articles is to add a list of inbound links to the end of an article. This allows the web user to follow inbound links (in reverse, so to speak) as easily as outbound ones.
A lot of apps that use Web-style linking (links embedded in text) can’t do this unless extra mechanism are in place for back-traversal of inbound links, Roam is a case in point—there will be others, but the main point it is not an automatic feature.
All that said, does the order of linking matter. In general, No, but consider:
- Consider ‘reading’ your work either in in-app preview or exported to HTML/MD/etc. Which seems the most likely direction?
- For reading use, you may choose to actually create a pair of (visually) explicit text links: A → B and B → A.
- You navigate forwards more than you back up but Tinderbox’s ‘Go Back’ is always there (but often forgotten).
- Don’t overlook Roadmap view (menu View ▸ Roadmap, or
⌘+⌥+⇧+R)., as a pop-over or stand-alone dialog to help navigation. IOW, don’t over think the link direction. - The link creation pop-over allows you to swap source/destination, i.e. the link direction at creation time. Maybe you started wrong, or was easy to trigger thine like in the ‘wrong’ direction, but can be fixed as point of making.
- Action code allows traversal/querying in either direction, so again you don’t have to over-think originally created direction.
If you want to export footnotes with their source text, see here.
HTH 
†. The content detail is slightly out of date but the main structure of the XML and the use of a linkbase (the <links> element) still remain.
‡. An example link: link tag