What are the consequences of wrong maintenance of Goods supplier for SAP GTS or Foreign Trade processes?

In case Goods supplier (GS) is different to the Vendor, it is very important information which needs to be maintained in the Purchasing documents so the Intrastat and Import process is correctly determined.

There are situations when your vendor is in Netherlands but his partner company ships the goods from China. 
No Intrastat | Yes Import

Or example when your vendor is in Macedonia, but his daughter company in Romania ships the goods.

Yes Intrastat | No Import

In case you would miss these Goods suppliers to be maintained in the Purchase order or Scheduling agreement, you would simply miss these entries in your Import or Intrastat worklists (they will be incorrectly assigned to different processes). In case goods supplier is not maintained the vendor is taken into account, but that would be wrong for both cases.

Ussually GS is maintained in the MM Scheduling agreement or Purchase order (PO) and it is static due to the Contract.

But still it needs to be controlled. You never know before the shipping papers arrives who is actually a Goods supplier. Ussually in case Vendor is short on production he needs to inform customer about different Goods Supplier.

The Goods supplier mantenance and its business process needs to be defined in the way – when shipping papers arrives, purchasing users needs to update MM documents respectivelly. It is hard and in some cases impossible, but still it shall be managed.

Where is the Importance?

Intrastat reporting

One of the Intrastat elements is:

e. the partner Member State

For intra-EU exports, the partner country is the Member State which is presumed to be the destination of the goods, i.e. the country to which the parties of the export contract have agreed that the goods will be delivered.

For intra-EU imports, the partner country is the Member State of consignment. This is the Member State from which the goods were actually dispatched to the Member State of arrival, according to the export/import contract.

For goods in transit, i.e. goods passing through a country or a Member State for purely transport related reasons (including consolidation of freight), the entry into or the exit from this country has no effect on the definition of the partner country.Source: National requirements for the Intrastat system 2018 edition
And it is influencing also country of origin:

If the country of origin is not precisely known, the probable country of origin should be indicated. If the origin is not known at all, the Member State of consignment must instead be declared. Source: Intra-Community Trade Statistics
Import process

Country of supply defines whether purchase order/Inbound delivery is relevant for Import before goods receipt worklist. In case you would miss to add non-EU country of Goods supplier in the PO, keeping only Vendor from EU, you would miss this entry in the Import worklist. Only possibility would be than for user to update PO with correct Goods supplier or to manually creeate Import declaration in GTS system.