What does it mean coming from Germany or any other Category A Country to Cyprus but with Transfer in Athens or Greek Airport?

According to the F.A.Q.’s Page on www.cyprusflightpass.gov.cy, the transfer in Athens is NOT considered a Country of Origin.
The Text Reads:

If your trip to the Republic of Cyprus does not constitute a direct flight but also includes intermediate stops / stops in other countries and / or you are a transfer or transit passenger, through airports of other countries, you should state, during the completion of your application, the kind of your travel to the Republic of Cyprus.

As Country of Departure you should register the country of origin of your travel to the Republic of Cyprus, stating the date and time of your departure from this first country.

In addition, the flight number and seat number (if available) as well as the name of the airline, must be registered as they appear on the itinerary of your last flight to the Republic of Cyprus.

The intermediate stop at an airport in another country without an overnight stay(s) is not considered as a stay in that country and therefore you should not declare it. On the contrary, the intermediate stop at an airport in another country with an overnight stay(s) is considered as a stay in that country and therefore you should declare it. It should be noted that in the case where your itinerary to the Republic of Cyprus involves an overnight stay in a country with less favorable epidemiological criteria compared to your country of departure (i.e. you depart from a Category A country and you will spend a night in a Category B or C country or you depart from a Category B country and you will spend a night in a Category C country) you will be considered as travelers from Category B or C Countries respectively and all the requirements for Category B or C Countries, have to be satisfied accordingly.

On the other hand, if you depart from a Category B or C country and as part of your trip you stay for more than 14 days in a Category A country, or depart from a Category C country and stay for more than 14 days in a Category B country, i.e. in countries with better epidemiological criteria compared to the country of departure, you should declare as your country of departure and the date and time of departure the country of Category A for the first case and the country of Category B for the second case.

Conversely, if you depart from a Category A country but within 14 days prior to your travel to the Republic of Cyprus, you have lived / stayed to a Category B or C country or if you depart from a Category B country but within 14 days prior to your travel to the Republic of Cyprus, you have lived / stayed in Category C country, i.e. in countries with less favorable epidemiological criteria compared to the country of departure, you have to declare as your country of origin and the date and time of country of origin, the Category A country for the first case and Category B country for the second case. However, you must, additionally, state the country (ies) where you have lived / stayed during the 14 days prior to your travel from the country of origin as well as the Country(ies) of the intermediate stations, if you will be traveling to the Republic of Cyprus, through Intermediate Country (s) with or without an overnight stay.

The categorization of countries and any change in their classification may be reviewed in the CyprusFlightPass online platform at the link https://cyprusflightpass.gov.cy/en/country-categories

It is recommended that you regularly visit this online platform for possible changes in the categorization of countries that may affect your flight to the Republic of Cyprus.

As the Situation evolves this Info can change. Best is to check on the Cyprusflightpass Website regularly.