I think there is a distinction here. The Bush "Funeral Train" was a special excursion train used to transport the president to his final resting place, but there was nothing unusual about the cars as they've been all over the system in excursion/business service. To that end, the train would be nice to have for your E8/9's, Heritage units, Big Boy, Challenger, and 844 FEF. What made this train different is the purpose of the excursion it ran and that it was headed up by UP4141, the SD70ACe specially painted to commemorate the George H.W. Bush Presidential Library (I haven't seen pictures of it headed up by UP4141 prior to this). To the best of my knowledge #9696 was "just another" SD70ACe with the "Building America" tag line and American Flag (which appears on other locomotives) -- I think the locomotive type, flag and tag line were important factors.
The Lincoln Funeral train was a special one-off build. As I recall, it was the then-equivalent to Air Force One, but President Lincoln never got to use it. Instead, it carried his body and family to Illinois. It was also pulled by different locomotives on different legs of the trip from Washington DC to Springfield, Ill. While it would be an interesting collector piece, it's use was specifically for the presidential funeral.
