When they retired the first round of Highliners, Metra actually called up a lot of museums and offered them dirt cheap to anyone who wanted some. IRM turned them down because the ones in the first batch were in awful condition, which is why they were weeded out first. Looks like IRM plans to get a set from the final round being retired now (how many original order IC cars are left, and will they be in good shape?). Two are on display at a depot museum in Mendota. FRTM also got the offer, but unfortunately Highliners aren't a good fit for the collection.
I think Boone and Hoosier just got so many cars because of the low price (possibly free), more cars than needed simply for preservation. There is a flood of carbon steel commuter cars retired since the 90s floating around without any market or purpose, and I am concerned about resources that have gone to purchasing, moving, and storing them that could have gone to preserving more interesting equipment. It is mostly not museums doing this, there seems to be a lot of railfan "entrepeneurs" who think junky commuter cars are worth more than scrap value.