The practical reason is to control sending of cookies. However, this can better handled by setting the correct domain (and path) on the cookies. This will greatly limit the cookie volumes.
One of the reasons I have seen is that someone decides to use
thisIsAReallyGoodName.com for some reason. It may seem like a good (marketing?) reason at the time. However, this results in domain bloat within the organization. These domain may go AWOL as they may not get managed as a corporate asset. This can and does lead to link breakage.
As you have noted, it also leads to a loss of brand focus. In some cases it can damage the image of the company. I see this kind of mixed domain names in a lot of phishing email, so I, like you, will be skeptical of their communication. This is not good marketing.
I also see non-existent sub-domains being used in email addresses. This is unprofessional, and tarnishes the image of the company. (At least one large computer brand has this problem.)