So what I got so far is, the XL ship designer (fine), and that custom modules are merely scripts put into a level that place images and work based on their code rather than an "injected" module as I was sadly hoping for.
I also assume by how the game was not meant to work with XL ships, it refers to that its fully operational BUT the game has the restraint as a method of limiting a tax on performance. Such as the physic interactions and calculations for large ships, the larger the ship, the more calculations and so, less performance. I am assuming it's that and NOT that if you build big, the game's performance drops exponentially due to that ship being a single "ship", I am comparing this to my multi-ship station that has multiple idle "ships" sit next to each other, the difference in performance impact I assume is similar, with the difference being due to individual calculations as a single large entity.
To put it short, I am assuming that making an XL ship in the editor has a similar performance impact to having a multi-ship such as the Space Station (it's not a "Nexious Space Station" just to clarify) and that only when you get REAL big, like bigger than my Space Station will there be a notable difference in performance between the two. If not, that's ideal as it means I can build larger on specific axis but have similar volume to the normal ships, resulting in basically unchanged performance.
Also real quick, how do I convert a "rar" file into a "dat" file. The process of adding custom modules as far as I have derived is, downloading an example ship that possesses the scripts and images, transfer the scripts to the desired mission editor save directly, and add the custom images as normally. My problem right now in understanding is how I can get that downloaded ship which has such assets to actually give me the assets, it's not a zip and I "want" a zip file to put it simply. Or am I missing something?
Also.. quick advice about that video (don't care if it's ancient), try being a bit more concise with your organization, I found it hard to keep track as to what you where doing as you bounced between windows (though you still did very well as a whole, this is just constructive criticism). An example to what I mean is, I found an easier time understanding information involving the custom ship editor than the way you moved files around. The editor information was all done inside the editor on a single window, the file jumping was between many windows with multiple tabs. So I won't be surprised if I am simply missing something.
Thank you all for the help.

The ship editor alone will make things easier for me, I build very detailed (in a purposed manner), so size is a mortal enemy for theming larger builds.
So to sum it up:
Ship editor XL: Performance is expected as normal, you have something with hundreds of individual pieces, of course the game will lag a bit. So the presence of my Space Station as a single ship has a near identical performance impact to simply "constructing" it out of multiple ships. Please tell me if this is not the case.
Custom modules: Download a ship that has custom modules, open the downloaded file to move around scripts and images accordingly, apply them in the editor, and account for where the modules are on the ship (the only part I am disappointed in, can't just place it in the ship editor with all scripts and images included in-game). The part I am stuck on is that after downloading the ship as a rar file, it's just a single rar file. Where are the scripts and images? (I am not too experienced in file management by the way though not incompetent, just inexperienced.)