I am not at all clear what you are doing with this.....

1) What skeleton are you using for the RIDER. This is the only skeleton you should be changing. The horses ALL use the same skeleton.

2) With the standard bearer...if you make him mounted, and use a cavalry rider skeleton, he naturally will be using his standard as a 'spear' or whatever. To really make that work as you want it to, you are going to have to either change the model so the standard and arm are not animated and remain fixed in position.... or else design a completely new rider animation to make him do what you want.

This is one of the limitations of using the stock skeletons for things they weren't really designed for.