Don't think this is really a shortcoming of SE as you call it.
Think about it once. If you have a assy open and parts activated then open a part through explore, or just right click and open, it knows its open in assy also. Now if your replacing a part with a part that already open. SE currently has no way to see which one is newer when saving assy. Remeber, when saveing a assy it's saveing what the pert current looks like in the assy.
I personally never have a file open and then try to replace a part with the part that's open, it's just a bad practice i believe.
Also, it's my opinion that majority, not all, of so called short comings are typically due people not knowing how to use the cad system. Every cad system no matter if it's ProE, SolidWorks and ect have it's short comings. Trust me, i deal with this on a daily bases almost
Solid Edge V20