COVID related travel requirements for train journey Austria -> Germany -> Netherlands

Entry regulations in Germany are listed on the website of the Auswärtiges Amt. There, it says:

No exceptions can be made for entry from virus variant areas. Those in transit from high-incidence areas and other risk areas are exempt from registration, testing and quarantine requirements under certain circumstances. This includes transit through a risk area without a stopover prior to entering Germany as well as transit through Germany via the fastest route, e.g. with a confirmed onward flight to a third country.

As Austria is not a "virus variant area", you do not need to fill in the digital entry registration, to provide a test result, or to quarantine if you are in transit via the fastest route. (If you have been in a virus variant area in the last 10 days, no exceptions apply to you and you have to provide a test result and quarantine and fill in the form. The list of virus variant areas is here. You can click on the English PDF link at the top and then, on the PDF, search the heading 1.The following states are currently considered as areas of variant of concern).

Quarantine regulations vary by state (Bundesland), so you would have to check every state that you cross. I expect that no state will make you quarantine if you are in transit: for example, in Bayern you do not need to quarantine as you can see in the FAQs here (search "Durchreise").

The government has decided on January 19th that soon medical masks will be required in trains, stations, and indoor places in general. This means that "community masks" made of cloth are no longer valid: only surgical masks or FFP2 masks are allowed. In Bayern, only FFP2 masks are allowed, though long-distance trains are exempt.

TL; DR

You will have to wear a surgical mask on the trains and in shops. For transit through Germany from a non-virus-variant area, leaving Germany via the fastest route, you will not need to quarantine, register, or even a negative test. However, some rules can change at any point and any federal state. Check the website of the Auswärtiges Amt. Bringing your negative test won't hurt, and having a couple of FFP2 masks just in case won't either. Regarding FFP2 or not, "doing as the Romans do" will probably help if you miss some new regulation.

For the Netherlands:

• You are required to present a negative test result

  International train and coach passengers will be asked to present a negative test result before boarding or during the journey, but at any rate before the first stop in the Netherlands. If they are unable to do so, they will be asked to get off the train or coach at the first stop after the border.

• Face masks are mandatory in public transport.

• After arrival, you need to self-quarantaine for ten days.

For Germany, no formalities are required as you're only in transit.

For the Netherlands, you usually need a negative PCR test (max 72 hours before entry) However, there's a loophole: travel to Düsseldorf or Duisburg and then cross the border by the RE19 train to Arnhem (so NOT an ICE or IC train), and you'll NOT need the test (SOURCE). From Arnhem, hop on any connecting train you like.