Thanks for all the feedback, glad that you found these tools useful @Rando.
I can see how this can be a little overwhelming at first, I only provided hints to plugin-based solutions. I believe that you mostly got things right, and hopefully the following lengthy explanation will help clarifying these concepts.
Some definitions
Inline tag: This is nothing more than a word in plain text that can be recognized by an automatic search query (for example, because it begins with a hashtag). Every word that starts with # is an inline tag (unless you change the default settings). Rich Markdown can recognize these words and highlight them, but these are just cosmetics; the inline tag converter can copy them into the list of Joplin tags; or inline tag search can extract all tagged paragraphs and display them in a panel. Ultimately, the tag remains just plain text (so you can edit, copy, paste and move it around freely), and will therefore be exported with the note no matter which way you do it. Each plugin that operates on these tags only searches for a pattern in plain text, and does so independently from the other plugins.
Inline Tags plugin: This plugin does 2 things: (1) It has an auto-complete feature that pops up in the editor while you start typing a tag; (2) If you select a tag from the list it will also add a corresponding Joplin tag, in addition to the plain text inline tag. This means, that if you skip the auto-complete (or "create new tag" option), it will not provide the second feature. You need this plugin only if you're interested in features (1) or (2).
Inline Tag Navigator plugin: This has a number of features, but we focused on 2 of them:
(1) It may convert all plain text inline tags in a note into Joplin tags. If you want this to happen automatically, you can define in the plugin settings a periodic conversion of all your notes (for example, every 5 minutes). While the Inline Tags plugin (the one from the previous section) converts each tag that you select from the auto-complete list to a Joplin tag, the plugin here operates differently, searches for all #-starting words in the note, and converts them to Joplin tags in a single action. This means, that even if you skip the auto-complete menu of the Inline Tags plugin (or remove the plugin altogether) the tags that you typed will still be converted to Joplin tags. This also means that notes that you wrote in the past and contain inline tags in their text can still be converted to Joplin tags in a single click. (As always, I'd be careful with converting all notes in a single click before testing a few notes and checking that you get what you expect from the plugin. Maybe also generate a backup of your notes first.)
(2) It can search for inline tags and display the paragraphs where they appear. You don't have to convert the tags in order to use the search, and you don't have to use the search panel (just hide it with the toggle command) in order to convert your inline tags. Furthermore, the Inline Tags plugin is not required for these features. It's indeed true that it does not search for Joplin tags at the moment, but if you consistently tag all your notes with inline tags (the tag list at the top of the note that I mentioned), then it will effectively search all of your tags in all of your notes, whether they were also converted to Joplin tags or not.
Rich Markdown plugin: If you're only interested in highlighting inline tags in the text (you're handling typing them manually, and searching for them using standard text search), then all you need is this plugin and none of the others, because each of these plugins operates independently on inline tags in plain text.
Another plugin worth considering is the template plugin, which you may use to create notes that already include the tags: placeholder. (It's generally a great plugin.) In any case, the plugins above allow you to choose any format to add inline tags, be that at the top of the note, bottom, or scattered all over.
Indeed, while writing the first reply it occurred to me that this could be something that you (and perhaps other users) would be interested in. This is a good suggestion, and I'll consider adding this feature. It's a little challenging, because deciding on a format to add the tags to the body of the note is something that many users will want to customize to their needs.
If everything is set correctly, any tag that is highlighted by Rich Markdown should be recognized by Inline Tag Navigator (unless it's a HTML note, or within a code block). If you have a specific tag that does not follow that, please share and I'll be happy to check.