I too am using different flower colors for different types of soldiers; in my case, purple for the hussars, and yellow for sailors. I'll probably continue doing that as new soldier types come out.
For your part, you may be creating a problem where none exists. As long as different flower colors are interspersed, I think the effect will look uniform and good. You might not want to use all six flower colors, but as long as you don't go overboard...
On the other hand, there's nothing as attractive as a uniform army. If you have one group with one color flower on the left, another with a second color flower in the center, and a final group with a third color flower on the right, that might end up looking almost the same as three different color uniforms. That might look good though, and if it doesn't, you can just intersperse them again.
Obviously, I vaccilate...

By the way, you're doing a great job with those Siflor flowers. I always have trouble with them, and consider them the worst part of basing.