Thank you for your answer Jaideep.

This is our current workflow.
Input - Quality Control - Raw Materials (this is how we receive the products)
There are already 2 transfers in my opinion. From Input to Quality Control and from QC to Raw Materials. Correct me if I am wrong here. We actually created operation types for this transfers (pick for QC as well as QC Pass & Store in Raw Materials)
Operation types: 1x Receipt and 2x internal transfer (Pick QC / Pass QC & Store)

Component Production for Semi-Finished Goods
Before we can produce the (Semi-)Finished Goods we need to produce a component which is needed for the Semi-Finished-Good.
I created a separate route for this.
Raw Materials - Staging Room - Production - Staging Room
Operation Types: 2x internal transfer (Pick for Staging / Pick for Production) + 1x Manufacture (Component for Semi Finished Good)

This Route is followed by 2 more Production routes.

WIP Production:
Raw Materials - Staging Room (this is the transfer which can only be done with full packages) - Production - Post Production - Cold Storage WIP
Operation Types: 3 x internal Transfer (Pick for Staging / Pick for Production / Store WIP) & 1 Manufacture (Semi-Finished Good)

Finished good production:
Cold Storage WIP - Production - Post-Production - Cold Storage Finished Goods
Operation Types: 2x internal Transfer ( Pick for FG Production / Store Finished Good) & 1x Manufacture (Finished Good)

At last we have the pick and Ship Route for the Finished goods as well
Cold Storage Finished Goods - Output
(1 Transfer and 1 Delivery Order)

Please correct me if I am wrong with this Internal Transfers.

Question 2
I somehow managed to turned it all around. Now the receiving route works but the pick and ship route has this problem now.
I flagged the 3-step-way on the warehouse. On the generated route i flagged only product categories and added the route in the corresponding product categories.
Nevertheless, the pick & ship step is in every product including the raw materials and semi-finished goods.
Would the be a workaround to just duplicate the route and delete the rules in the original route?

Thanks for the elaboration concerning transfer of entire packages. I will flag this for the Operations up until pick for production where the packages are consumed according to the production need.

a). Yes, it is possible to duplicate routes and modify the rule. You would need to be cautious to the sequence number of the routes. This field is visible while on developer mode.

b). In theory it is possible to use just 1 'internal transfer' operations for the stock movements between internal locations. In practice there are variations between operations (even though they are type internal transfer) eg. bar codes vary, transferring package or limiting, propagation, customer or vendor name, return operation etc

To change an operation type on a route, go to the rules in the route and change operation Type. eg. To change 'Pick' on the 2-step delivery route, select the rule WH/Stock to Output rule and change the operation to 'Internal transfer'.

Material transfers to and from production can also be managed using multi step manufacturing routes if the transfer itself needs to be managed or consumption location selected directly on the MO. Another option would be to create multiple Manufacturing operations with different source & destination locations and this can be directly selected on miscellaneous tab while creating an MO eliminating need to create internal transfers.

By not knowing details of your operations (no of pickers/ operators, volume of movement, visibility and specific requirement for moves etc) it isn't practical to suggest or recommend one way over the other. Both are correct and flexible to configurable

Hope this helps to clarify.