I...honestly can't even remember how the hell I figured this out, but I successfully modified the Character Select: Leukon Knight code to instead load a weird type of SC card that is basically a duplicate of a real one, but with the commander's appearance, and the commander's name. I think I mostly just switched the card ID in the code until I got the result I was looking for.
Regardless, these codes I made are, AFAIK, completely stable and balanced, in the sense that, 1. I've never had the game crash when using them, even offline, and 2. The stats are identical to the story char they represent, meaning it's purely cosmetic.
The added benefit of these codes vs the Online-only one posted in the server info page is that once a deck with one of these is made, it actually saves, and from then on can be loaded as normal, meaning you can make a duplicate of your favorite Silfer deck with Silfer/User, and load it only when you want to use said deck with the Commander skin. I haven't tested them in multiplayer, but they SHOULD work, I hope.
With Ep3 Plus it also works without the Deck Corruption Code, meaning once saved you can load it up and use it even without a single code loaded!
Note that due to Ep3 having practically no active AR code devs these days, and the vast majority of Ep3 codes being of dubious quality, I can't confirm that this also works with the Ninja skin, the Sonic Char skins, Red Ring Rico, or if they're even on the Ep3 disc, Flowen and Elly, as none of the codes I found were capable of actually making my skin change to one of those, at least on Dolphin; in theory, making a max height HUmar be your commander skin and then finding a working alt skin code should allow for those alt skins to be used over top of the SC cards, but as the alt skin codes I could find are all broken, I can't confirm it's even doable.
Anyway, here is the code, and the specific modifiers needed for loading the /User variants of all 24 Story Chars:
0427b100 386002XX
Possible values for XX:
CC: Orland/User
CD: Kranz/User
CE: Ilnois/User
CF: Sil'fer/User
D0: Guykild/User
D1: Kylria/User
D2: Lura/User
D3: Break/User
D4: Saligun/User
D5: Relmitos/User
D6: Viviana/User
D7: Teifu/User
D8: Stella/User
D9: Glustar/User
DA: Endu/User
DB: Hyze/User
DC: Rufina/User
DD: Peko/User
DE: Creinu/User
DF: Reiz/User
E0: Rio/User
E1: Memoru/User
E2: KC/User
E3: Ohgun/User
To use it, load the game with the code and speciific variable (not more than one, though), load up Free Battle mode, go to deck editing, and create a new deck (pick the char that matches the variable); once the deck is finished, save it and you should note the lack of a portrait over the deck; this indicates it worked. Exit out, restart the game without the code, and then load the deck as normal to play as your Commander with the stats of your chosen character!
Note that this only works codeless on PSO Ep3 Plus; you'll need the Deck Corruption code to use it on a vanilla copy. Use the following if you insist on using an unpatched copy of Ep3:
0430a7e4 38600000
0430a7e8 4e800020
Despite the name, the DCC is more like an M code for card mods like this. Without it, vanilla Ep3 will delete all cards and decks that have unreleased and/or unplayable flags set, thus making it impossible to use card mod codes. Ep3 Plus's latest builds already disable that feature, so it's more optimal to use Ep3 Plus if possible.
I hope you guys enjoy these codes 
