So you have to use a combination of things done with HW2. Take a good look at the PDS system, use that sytem to trigger an animatiom and emulate what gunmad mod does to simulate moving parts atleaft for Valkrie's.
So during sustained flight there in fighter mode, when they engage a target this switch to gerwalk mode and for defense agains in coming missles battloid mode. I know its not as easy as it sounds but if you position the hardpoint on the fighters right and add a few moving parts during the transformations, it wont matter that the hardpoints dont move when fiing plus it waill all be happeneing so fast none will really notice it. An option with the larger transforming capital ships, disengage the other weapons and hardpoionts during the firing sequence this was it won't look funky