If a ship does have built in weapons, then logically these weapons would have to be better somehow than it's equivalent (assuming such exists) installed normally.
Such as being more Flux efficient, more damaging, possessing qualities/abilities the normal one doesn't have, etc.
thats not actually necessarily true, filling out what would otherwise be slots full of better guns with worse guns would make for an interesting way to tone down the balance of what might otherwise be an overtuned ship.
like you could build a frigate with 5 guns designed explicitly to be unbeatable in a kite battle, then make 2 of its 3 forward facing slots built-in mortars so it only actually gets 1 slot to use for kiting. those mortars would still be useful for a ballistic kiting ship, since its kiting smalls are all kinetic so it has a built-in "close in & break armor" option, but that will never be as useful as 3 railguns, AND, having "close in & break armor with mortars" be always a part of the ship's kite would mean it has a baked-in oppertunity for ships it kites to get hits in, & if the ship never gives them that opportunity then its giving up something for it (operating time spent wearing thru armor with railguns instead of mortars)
in fact, one of my favorite ships is a modded ship with 6 drones that shoot at your target when you do, that gets to be far better than it would otherwise get to be because theyre all tac lasers. if it had open slots in their place instead of built-in the ship would have to be weaker to the point it wouldnt be fun to me to play, but since i like the terrible guns it has built in and it get to be OP otherwise, its a great ship