Directory Opus is capable of doing practically anything you ask in your requirements. But is far from free. Or open source.
And why does a file manager have to keep track of indexed files and their content? Database software is designed to do just this. A file manager would become unwieldy quick if it would have to keep track of indexed content. The only thing a file manger needs is an easy way to access the data stored in the index. Tools like Everything are way better/faster at finding files with specific content.
Besides the unwieldiness, how often does this index needs to be updated? On a system where not much happens regarding files, the need of creating/updating a file content index isn't high. On a system where lots of file changes occur, an index would obsolete very quickly. Indexing normally puts quite a strain on your drive. Even SSD's suffer in performance when creating/updating a file content index.
A file manager really isn't the optimum tool to manage indexes.
Directory Opus and Total Commander allow for scripting, so you can create your own options/buttons to have access to indexed content. With the other tools in the set you consider, I'm not sure if scripting is even an option.
Total Commander is also not free or open source. Multi Commander
comes quite close in features regarding Directory Opus/Total Commander and is free. Last time I used it, the quirks encountered were enough to make me stop using it. So, it might not be such a great option for you too. Still, its feature-set is really impressive. And it has been at least a year since I tried it last.
** edit **
There used to be a quite usable forum available on that website, but the links are currently mangled. The forum links point to a subdomain that doesn't appear to exist anymore. Manually replacing the subdomain in link: forum.multicommander.com/forum to www.multicommander.com/forum
will show the content of the forum, but in a very messy way.
** edit 2 **
Diffing file content is also out of the scope from any file manager. While it may sound logical that a file manager should be able to do diff file content, diffing file content is actually very difficult to do. Sure, very basic text files are not too big of a deal. Although when text files become larger and have the same content, but in different order, it trips even the best Diffing software. Diffing other file types, that usually entails the diff software to convert that file format to a simple text format, before the actual diff occurs. Conversions often end up in content that is in the incorrect order, tripping the actual diff up.
Haven't seen much improvement with this over the years in software like Beyond Compare, ExamDiff Pro or WinMerge (free). And this is dedicated software, made by knowledgeable people for their living. The maintainer(s) from file managers don't have that expertise, so whatever diff capability they mange to add to their file manager, it will be a pretty poor implementation. And you'll likely just go back to the tool you always have been using to do diffs. Resulting in unnecessary cruft inside the file manager.