How to properly glue wood to a silicone mold to later fill with another material?
Silicone works well as a mold material because virtually nothing adheres to silicone other than silicone.
CA glue may not be a good choice, as it certainly will not adhere, but also may damage the surface of the mold.
Your best option is to attach the wood to an outside jig or bracket of some sort, which has reference points to the mold that are not adhesive dependent. For example, if you can encase the mold in a box of plywood and drill holes in the plywood for attachment, the insert with an extension arm would drop into the mold in the correct position once the holes on the outside align with the arm.
Without drawings of the mold and insert, I can't generate a mock-up drawing. Words will have to suffice.