Transit in Amsterdam from non-Schengen to non-Schengen

You won't have to leave the non-Schengen area of Schiphol.

While you can say the D gates are "mixed", it's a little misleading. The fact is the D pier has two levels:

• Lower level (D2 through D57) non-Schengen
• Upper level (D59 through D87) Schengen

You can see the arrangement on the map: https://www.schiphol.nl/en/airport-maps

This is the lower level (level 1). The non-Schengen concourse forms the upper half of the image, and you can see that there's the passport check area separating it from the Schengen concourse (bottom left). The lifts/stairs to the upper level (D59-D87) are marked right next to one of the passport check areas. The non-Schengen concourse continues past the top of the pictured area to piers E through G (similarly, Schengen piers A through C would be further down on the map).

The terminology on the Schiphol website seems coherent. They consistently use “Schengen or EU” precisely because those are two different set of countries and the relevant recommandation covers the whole EU (and not only Schengen countries within the EU).

Even the Dutch government webpage where your quote is from seems reasonably clear. The rules are about entry in the EU as a whole. The paragraph you quoted is from a list of exemptions. Full quote below:

• You are travelling through the Netherlands to a non-EU country. You must prove that you have a connecting flight to a country outside the Schengen area. The connecting flight must depart within 48 hours of your arrival in Amsterdam. You must not leave the airport’s international transit zone in this period.
• You are travelling to an EU country/Schengen area country via the Netherlands. You must be able to show you have permission to enter the EU country/Schengen country in question. You can do this with a note verbale from that country’s embassy, for example, or another type of document that proves you can travel there. If you do not have such a document, the Dutch border authorities will determine whether you may travel via the Netherlands. Without a document showing you have permission to enter the EU country/Schengen country in question, you are advised to fly there directly and not via the Netherlands. If you will be making a short stop at a Dutch airport you may need an airport transit visa. If you are travelling to another country via the Netherlands, you must present a negative test result.

The use of the words “Schengen area” in the second sentence of the first bullet point is confusing and sloppy but clearly this bullet point doesn't apply to your situation. If you travel to an EU country, it's the second bullet point that applies. The bold typesetting supports this interpretation too.

Obviously, this doesn't line up exactly with the way the airport is setup or the way regular immigration checks are conducted and leaves non-EU Schengen countries like Norway in an awkward position but the intent is still clear: The Dutch authorities are entitled to ask for evidence that you are allowed to enter Croatia and qualify for an exemption to the EU entry ban beyond that for transit. Any of the other exemptions listed on the page should be enough but you cannot rely on regular transit rules or the lack of permanent passport checking booth in the transfer area to satisfy this rule.

You might be able to transit in Amsterdam. There is an EU Entry ban (hence the EU/Schengen confusion) Basically you can transit if you can prove that you are allowed to enter Croatia. source

You are travelling to an EU country/Schengen area country via the Netherlands. You must be able to show you have permission to enter the EU country/Schengen country in question. You can do this with a note verbale from that country’s embassy, for example, or another type of document that proves you can travel there. If you do not have such a document, the Dutch border authorities will determine whether you may travel via the Netherlands. Without a document showing you have permission to enter the EU country/Schengen country in question, you are advised to fly there directly and not via the Netherlands. If you will be making a short stop at a Dutch airport you may need an airport transit visa. If you are travelling to another country via the Netherlands, you must present a negative test result.

Thanks for your thoughts on this. I was able to successfully transit AMS Schiphol. As soon as I left the plane, however, I was a bit scared because there was a passport pre-check, but all they did was make sure I was the person on the passport. Plus there was a security checkpoint too, and after that, I was free to walk around the non-schengen area of the airport. Immigration in Croatia was a bit tough, but I had all the documents the officer could ever ask for, and he went as far as calling the airBnB guy. Thank god he picked up.

Thanks for your help!!