Color charts differ depending on the article of clothing and faction. The Klingons, for instance, do not have access to the same amount of colors as the Feds do. For some reason they lack the colors green and purple, though such colors have been worn by Klingons in canon.
Also, Off Duty color charts differ from the other charts and give access to an even wider variety of colors. Ditto for the MU Sash color chart.
If your charts for the displayed costumes are different, please take a screen shot so that I can see. Maybe I can explain why.
As for the customization options, I likely have all the same options you do, I just don't use many of them here because this is a guide to canon uniforms and much of the accessories are not truly canon.
I know that there is variation when it comes to color and faction and The new tribble update fixed it.
All officer uniforms have a division colored stripe on the outside of the legs on the trousers or skirt that matches the shoulder strap and service bar, except for command branch, whose leg stripes are red and not white.
While these outfits aren't exactly canon, they are quite close to some of those worn by cast members in the various series and films. Here's a few mock-ups I put together using contrasting colors that can be seen in TNG, VOY, DS9 and the TNG Films and a few others that are copies of those seen in the game.
The important thing to remember is really contrast. The ST costume folks liked to use a lot of pastels and put them against darker shades or bright foil trim. Earth tones were usually broken up with bright colors. Cool grays were usually contrasted against dark reds or violets.
Anyway, here's my take on them. Hope you all like them.
Really like those off-duty uniforms! They actually look like things I'd see people wearing in Ten Forward or on the DS9 Promenade. I would love to see more of what people have made, if anyone else can add to these, in terms of this style of off-duty uniforms, too.