I don't quite understand why your main requirement is the format in which the program stores its genealogy records.
I can see the format being a requirement if you want direct access to the data and want to be able to manipulate yourself in programs that you build. In that case, a program like RootsMagic holds its data in an SQLite database that any database tool should be able to access. Other programs use other database formats that are often easy to breach. But this just doesn't seem like a time-effective way to manage your genealogy. If the tool itself is not good enough for you, then you're going through a lot of work for limited gain.
If you are looking for tools that are "feature-rich, agile and extendible", then you are saying that you want a powerful tool that is extendible, and in that case the data format should hardly be a concern. For this, any tool with plug-in capability or an ability to extend itself might be suitable.
You mentioned Gramps, and if you're the hacker type, you might best spend your time getting involved in that. They have a big community, and rather than just writing code for yourself, you can help everyone.
Some programs have plugins. Family Historian, for example, has a public plugin repository. People can contribute and use other people's plugins.
But maybe, in your case, what might be best for you is any website-based software, that loads your data up to your website. Most use PHP with MySQL databases and you get complete access to all the code and database and you can enhance it, extend it, and get it to do whatever you'd like, including extending the MySQL data structure if you so desire.
Some programs you might choose for this might include:
The Next Generation, by Darrin Lythgoes, which will build your site from a GEDCOM file. It does require you start with a GEDCOM, but you can then take it from there.
PhpGedView, which takes it a step further and allows you to edit your data on your online site. It is also Open Source and you can help with its development (which has slowed down in the last few years). There are other systems like PhpGedView, and some based on it if you look around.
Gigatrees - by Tim Forsythe is a really well thought out website builder and editor which has more capabilities built in than most. If anything might suit your needs, this one might.
WikiTree - You might want to try a wiki format, which may provide you with the open, extendible type of data structure you're looking for.
If none of the above are good enough for you, and you want the ultimate in programmability and complete access to the GEDCOM database which you can extend in many ways, then I'd recommend the Lifelines program, originally by Tom Wetmore, which has since been made Open Source and has a community maintaining it.