Open source. The Bioconductor project has a commitment to full open source discipline, with distribution via a public subversion (version control) server. All contributions exist under an open source license such as Artistic 2.0, GPL2, or BSD. There are many different reasons why open source software is beneficial to the analysis of microarray data and to computational biology in general. The reasons include:
We try aggressively to require strictly open-source licenses, but a limited number of packages have non-open-source licenses for historical reasons, overlooked vetting on our part when the package was accepted, or occasionally other considerations. I encourage you to contact the package authors directly and express your dissatisfaction. I will soften the wording on the about page to make it more consistent with reality than with aspiration.
I think you are confusing 'a commitment to' with 'an absolute requirement of'. We strongly recommend all incoming packages be released under an Open Source license. However, not all package authors are able to comply with that, for various reasons. As an example MotifDb IS Artistic 2.0, but there are some data that come with that package, from different sources, that are under a more restrictive license. The other two you mention are free for academic but not commercial, for whatever reason.
I don't think you have missed any big warnings, but I don't really know what you mean by that. Warning about what?