Are you sure that these are mold spots? Mold or mildew is usually white/grayish. These spots look more like a discoloration to me.
If it is mold (I really doubt it) you can use a leather conditioner that contains a fungicide and is Ph neutral to kill the fungus. If it's not a show saddle go a step further and spray it with athlete-foot-spray if you want to make sure
PS: love your bucksin mare! :)