It's a mess for everyone designing SFF cases without having the budget or contacts to have a hands-on experience with every card from every vendor in current generation. If you don't have a list with actual measurements for each card measured the same way, it's hard to set a cut-off dimensions at some specific arbitrary spot because some of the cards that you think are inside may be outside because the dimensions were measured excluding bracket.
The worst case scenario is that you assume specific set of the cards to be exactly fitting and then most of them do not fit because of dimensions being not what you expected them to be.
At some point I thought that maybe the solution for this problem would be to force everyone to have the cable connectors at the reference PCB height line, so for any oversized/taller cards at least the oversize wouldn't affect the space for cable moving as well. Some vendors do it this way, but not everyone and a lot cards keep being oversized with connector placement shifted.
There's this saying going like "we sent people to moon 50 years ago and yet here we are struggling with centering an image on the website" which makes this CSS analogy quite good here. We could go forward with the SFF form factors a lot faster if the approach was to solve problems instead of ignoring them, but here we are struggling to explain someone how big is the object he wants to buy.
I think it's just the business/marketing approach to doing things: They focused first on those who want to have a simple choice while also limiting this to a close group of partner companies, so it's just a bean counter approach to try and gain whenever you can and gains here are not letting others in.
