While creating or editing a related product rule, it's possible to choose a Custom Position for the Related block. Once this option is selected, the module automatically generates a code which you can insert into a preferable layout in order to place the block in a desired position. The code appears in a Block Embedding box:
In this case, however, you no longer can specify the product pages this block will appear on. Due to that, the rule does not get assigned to any specific products and, therefore, does not allow specifying certain options. Specifically, you will no longer be able to set Source Type or apply 'Same As' condition which are otherwise available for editing under the Products to Display tab.
Here you may see the comparison between the settings for the Product Page position:
And the Custom Position:
This happens since both Source Type and 'Same As' condition require the module to get attribute values from the current product and show products with the same values. But as product details are unknown in case of the Custom Position setting, the module cannot retrieve this value. This logic is expected from the extension.