That's exactly right and I think it's no much "preferring", rather than getting different deals from these companies like Microsoft. MS has already been caught specifically, but also I think that this phenomenon is hardly exclusive to software, it's just part of how the government, or rather the individuals in government, go about their business. In the third world it's practically an open secret, and I don't have doubt that basically every government works like this.

Also, large companies offer quite robust support, deals to implement specific features, compliance with different regulations, etc. I know from experience that one thing I like about dealing with large entities is that they have many corner cases already figured out.