Consider the overhead involved in maintaining and packaging your own code base while still including updates from origin. Wouldn't it be much easier to submit a merge request so that you could just apt-get install the package and not worry about your own custom branch, not to mention feedback on your change from a much wider audience who are familiar with that code base? And then there's the fact that you're exposing yourself to liability that, again, would be solved by that merge request. It just seems like a lot of the ones that do, do it out of ignorance rather than malice.
I don't disagree that companies need to build up assets, but I think for most companies including SaaS ones, those assets are systems which are comprised of unmodified FOSS software used in [sometimes not] innovative ways.