Yes, this has been reported.  I think the reason it is currently done like this it is to do with what new accessory overwrites an old accessory.  Maybe it could be fixed by making the first new accessory you add overwrites the first designed accessory, with the exception that if you put the same accessory in, it would completely replace the one of that type in unit design (ie. you wouldn't get 2x the bonus), and so on for numbers two and three.  But any of the same accessory would overwrite the same accessory of the designed unit, no matter which slot it is.  But this would need to be explained in the tutorial, definitely.  Of course, this makes the order of designed accessories important, as number 1 would get replaced before 2 and 3, unless you are using the same accessory.  This would all need to be explained in the tutorial.

Alternatively, we could click on the accessory we want to replace from the designed list after we put in a new accessory (so it would be two steps for each accessory you equip).  If you already have that accessory, there would be a message that you can't have two of the same accessory equipped at once, and this would overwrite the one of the same type in the designed accessory.

Of course, no matter what is decided, it would have to be clearly communicated in a detailed tutorial that would be put in a prominent place so everyone will see it.  Also in the tutorial it would need to be mentioned that if there is nothing in a particular inventory slot, it would default to the designed weapon/armor/accessory/mount etc.  The current system is less than ideal because you can have two of the same accessory and get two times the bonus, and have up to 6 accessories total.  I think it will get changed before release.

Sorry for that wall of text!  I wanted to cover everything.