Are you... are you really saying that it's SE's job to arrange the hotkeys and skills in a good way so the player isn't "forced" to costumize? That the standard setup for both hotkeys AND skill arrangement should be sufficient to work with on all classes?
Everyone has different preferences, everyone clusters skills in a different way, has different hardware and different physical capabilities and limitations so of course you need to build your own setup, not just in FFXIV but every MMO. Things like fixed hotkeys with automatic and good skill arrangement might work in games like LoL, HotS and OW because you only have a handful of skills and the game's focus is a different one but for MMOs it's a completely natural thing that after gaining a couple of skills you notice which one you frequently use and how you would prefer your hotkeys, so you make your own setup. The skills are placed in the same order as you get them, how you prioritize them is up to you, not for SE to know in advance.
You have the option to costumize for a reason. The standard layout just gives you a general idea about how the UI can look like but things like differently sized and placed party windows for the different roles, hotbar settings, hotkey arrangement and general sizing and placement of other UI elements is of course completely up to you. As it should be. The standard UI and seetings work for almost nobody and that's not because it's so bad but because everyone wants it completely to their liking and their prefered settings vastly differ from each other.
I know as many people who would NEVER bind skills to A/D or Q/E as people who only use QWE for movement and bind the rest. Or people who feel completely fine using only mod keys + 1-9 while others abhor it.
Wether you want a 1x12, 2x6 or 3x4 layout is purely aesthetic and doesn't affect they way you bind or use hotkeys AT ALL.
You don't have to use 1-´ for one hotbar, you can set the hotkeys whichever way you like regardless of hotbar design. I'm starting to think you have some fundamental misunderstanding about how hotkey and hotbar settings work. You're not maximiszing anything by chosing 3x4 over 1x12 or 2x6. You could put a really tiny hotbar somewhere you don't even see it and still use the skills. Some people even do that because they don't need to see skills that don't have a cooldown.