I feel the same way. The Short mags were designed for the short actions and when placed in a long action several things happen that can be problematic.
First thing is the COAL. If you extend the cartridge length, the chamber has to reflect these changes. Feeding is not as good in a long action because the short case does not fit it well and tend to jump up before the bullet is started in the chamber. I have found that when building a short mag. it feeds best with a center feed mag box in a short action.
The obvious thing to me is that if I want more case capacity than the short mag has, I go with a bigger case and a long action. If a cartridge design does not produce what you want, go with one that does and build it in the appropriate action.
One of my short mags is a 338 RCM and I built it on a Model 7 Rem for a light, handy thumper. It will match the ballistics of a 338 Win Mag with a 200 grain bullet in a short lightweight rifle (7 pounds fully dressed and ready to hunt). The down side is that the recoil is brisk. I also hammer pigs with the 225 grain bullets.
All of these things should be considered when building one and you must live with your decisions, So be careful and build what you want.
Just my opinion
J E CUSTOM