Look at it this way, Jump engines are finely tuned for a certain ship size, they operate in one short burst then have time to cool down. Whereas a jump gate is massively overpowered to the extent that any size ship can fit through, and support nearly infinite volume of traffic, whatever physics bending tricks a gate needs to operate in thus way would surely have severe side effects to not only electronic systems but one should assume also biological entities. Whereas a military vessel needs to avoid as much as possible anything that could affect highly sensitive and dangerous equipment, even to the extent of their engines being a tenth as powerful as commercial drives, but being far more sensitive, redundant, and one would assume safer.
