Unfortunately only modded ships out there were done by Admins a long time ago, mostly during Red Scenarios or as a reward. There are very hard to obtain these days, very expensive too. Though some of the things you can probably RP in scenarios if your GM agrees to it, in case of White Scenarios. Though for stuff like smuggling departments I wouldn't think you'd need permission, you can RP the interior in any way you like.
It's worth noting that there are indeed plenty of cool ways to RP all sorts of mods. My Adz has rebuilt engines that allow it to move as fast as any cap ship except the mythical CR-92R, an enhanced targeting system for the ion cannons that makes it better at disabling ships than any other ship its size, a dedicated droid bay that enables all sorts of unique droid usage and a large section of the ship dedicated to R&D. I don't need to make claims that the ship is better than the standard stats because all Adz are that fast, they're the only ships in their class with ion cannons, droids don't require bays and supposedly all ships will be able to mount R&D tables when that's enabled, so all you need to RP that is a room set aside. The Darkhorse also has docking claws salvaged from a pair of Gamma class shuttles to be used for boarding purposes, but again, these aren't necessary for docking. All ships can dock so you're free to create whatever story you like about your ship's docking abilities.
Basically, you're free to make any sort of cool claims you like but the better ones are more consistent in that they don't violate the stats the ship already has. There are no stats for hidden smuggling compartments so of course you're free to create whatever you like about that. You can even use some literary license about how much capacity your ship has, though that won't change the way it transports in game.
My psychiatrist told me I was crazy and I said I want a second opinion. He said okay, you're ugly too.