You have defined why some companies don't let you keep your miles, and why many require you to book through a service, be it in house or one of the majors like travelocity business, where the employee does not get to make those decisions without approval.
See also this thread which has a similar discussion about people no longer able to choose who they fly
http://www.flyertalk.com/forum/trave...h-pennies.html
and this one about the company either keeping the miles or requiring employees use any they obtain on company travel for company travel
http://www.flyertalk.com/forum/miles...any-miles.html
While both may not be that common, they are way more common than they were not too long ago.