Magento 2 is incredibly customisable so not all apps and add-ons will put shipping instructions into the same field by default but you should be able to edit Magento to put your instructions into any field you'd like.
StoreFeeder will automatically try to pull shipping instructions from the following section:
- items -> extension_attributes -> "shipping_instructions"
So if you would like StoreFeeder to import your shipping instructions and place them into the special instructions section against the StoreFeeder order please make sure your instructions are put into an Extension attribute against the order called "shipping_instructions"
For some couriers we will send them the special instructions for delivery instructions.