When it comes to tax jurisdictional grouping of sales income Link My Books relies on the information in the Amazon VAT Transactions Report being accurate.
Not only is it important for you to enter all of your VAT registration numbers into seller central, you also need to consider opting to tax distance sales immediately when you register for VAT in other EU countries too.
Opting to tax distance sales immediately means that you opt out of any thresholds for distance sales to that country.
"Both VAT Calculation Services and VAT Services on Amazon assume that the Seller has opted for taxation in the country of arrival of their delivery as of the moment the Seller possesses a valid VAT registration number (provided by the Seller in their Seller Central account). This implies that an EU cross-border sale of goods to consumers (distance sale) will always be taxed in the EU country of arrival of the delivery ('destination country') if a valid VAT registration number for that country is available.
The general VAT rules that apply on distance sales state that these sales are taxed in the EU country of dispatch of the delivery ('departure country') as long as the Seller has not reached a certain threshold of distance sales performed to a specific EU country. However, it is possible for the Seller to opt to tax their distance sales immediately in the arrival country. Therefore, where a Seller has not exceeded the distance-selling threshold for one or more of their VAT registered countries, the Seller must ensure that they have duly informed the relevant tax authorities to immediately tax their distance sales in the EU country of arrival prior to enrolling for VAT Calculation Services."
Reference: https://sellercentral.amazon.co.uk/gp/help/help.html?itemID=202084570&ref=efph_202084570_cont_home (Section 5.5)
Since Link My Books relies on the information in the Amazon VAT Transaction Reports being accurate it is important that sellers ensure that they follow the guidance from Amazon above.