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The 'German' rules are, in reality, the rules of the individual Federal states (Länder).
As your first source also states:
Regulation of the quarantine obligation falls under the jurisdiction of the Federal Laender.
Both your second source (Nordrhein-Westfalen) and the corresponding Berlin law use the word aufgehalten, which in the English version of the Berlin law is translated as who were in. The word Durchreise (transit) is later used in § 9 for persons travelling through Germany/Berlin by a direct route.
Berlin: Part 3 §8 (English text) (German text)
(1) Persons who enter the state of Berlin by land, sea, or air from another country and who were in a risk area listed in subsection 4 at any time within the 14 days before entering the state of Berlin shall be obliged to go directly to their own home or other suitable accommodation immediately after entry and to remain there without interruption for a period of 14 days after entry;
...
(2) The persons included in subsection 1 sentence 1 are obligated to contact the health office responsible for them without delay and to report that they are subject to domestic quarantine according to the conditions described in subsection 1.
...
Similar rules apply when traveling within Germany through high risk areas.
The health authorities, based on public statements made in the past, do distinguish between driving directly through an infected area and those that stop for a meal in a restaurant where contact with others are possible.
A train stopping at a station within a high infected area, where passengers from that area can get on or changing a plane at an airport within a transit area where others from the infected area can also enter - will probably be considered situations where an infection is possible by the responsible heath authorities.
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In addition to @MarkJohnson's answer, you'll want to check the exceptions (Ausnahmen) articles of the relevant Land's legislation.
Yes, the rules apply, but these rules do have several exceptions and/or alternatives to quarantine.
You'll have to notify the Gesundheitsamt in any case. But:
the linked Berlin and NRW rules both accept a fresh (up to 48 h old when entering the Land) medical attestation with negative SARS-CoV2 PCR test result that states that there are no indications you have Covid.
They also allow a PCR test done in Germany to shorten the quarantine.
Both have a provision that the Gesundheitsamt can grant exemptions from quarantine on judging the traveller's interests and the particular epidemiological circumstances.
As an example excerpt form Berlin regulation §9
(3) Not covered by § 8(1) sentence 1 are persons who have a medical certificate together with current laboratory findings in German or English confirming that there are no indications of infection with the coronavirus SARS-CoV-2 and who present this certificate to the competent authority without delay on request. The medical certificate in accordance with the first sentence above must be based on a molecular biological test for the presence of infection with the coronavirus SARS-CoV-2 carried out in a member state of the European Union or another state published by the Robert Koch Institute and carried out no more than 48 hours before entry into the Federal Republic of Germany. The medical certificate in accordance with sentence 1 shall be retained for at least 14 days after entry.
(4) Besides the exemptions covered in subsections 1 to 3, exemptions from § 8(1) may also be granted in duly justified cases, provided that this is justified in the light of all interests involved and epidemiological considerations. In particularly urgent individual cases, the Senate Department responsible for health may grant an exemption pursuant to sentence 1; the responsible health office shall be informed of the exemption.