For sake of posterity, the short answer is that MapInfo and FDO (AutoDesk technology) are far removed from any development with SQLite, compared to the members of the SQLite Consortium. MapInfo and FDO (AutoDesk) would be contributing binary to their downstream users, via their products and services.
Spatialite is specked under a triumvirate of licenses--Mozilla Public License, GPL, and LGPL. QGIS (via the Qspatialite plugin) is the most significant user of Spatialite, seeing its preeminent usage compared to other applications, they contribute code upstream AND binary for users downstream..
Upstream of Qspatialite is Spatialite itself, controlled at http://www.gaia-gis.it/ This is where the development occurs of the deFacto standard. Spatialite_GUI, a simple executable that requires no installation, is the recommended executable to target design usage with. IF the Spatialite database isn't designed to work with this product, Spatialite_GUI, then its a "non-standard" version of Spatialite.
It's worth noting that SQLITE is the overriding database executable, which is public domain and therefore without any license at all. Spatialite extends SQLite. The chief developer of SQLite is Dwayne Richard Hipp. SQLITE has established the high reputability, trust and usage from major corporations.
A portion of the development is sponsered by the SQLite Consortium, which currently includes Bloomberg, Mozilla, Bently, Nokia, Adobe and Oracle. The SQLite Consortium is the deFacto Standardization of the SQLite database executable, located at http://sqlite.org If an sqlite database isn't designed to work with their executables, then it's a "non-standard" version, or fork, or SQLite.
Of note, I'm not seeing that commercial GIS leaders such as MapInfo, Autodesk, Safe Software or Esri are part of this SQLITE Consortium.
SQLite can easily store spatial geometries without being extended by Spatialite. But, Spatialite adds the ability to query the SQLite database based on spatial relationships, rather than just standard data value queries. If you don't need to query based on spatialite relationships, then SQLite (by itself) may be all that you need to store an archive of GIS data.
(Edit 2021): As of 2018 - SQLite can do many spatial relationships by itself using the GEOPOLY extension: https://www.sqlite.org/geopoly.html. If you wanted to limit dependencies, it may be worth investigating. I can't speak to its performance yet, or a feature comparison, but it seems to provide SQLite with a fairly decent spatial capability.