Can a non-EU citizen get a connecting flight from Japan to the UK via the EU during the Covid-19 pandemic?

Many changes can happen currently in a month (likely looser restrictions for some countries, but can also be tightened if the numbers require it); so don't rely on current information too much. Always check with your airlines and the border authority before travel.

For France, transit is possible only for returning to country of residence/origin. The check of the certificate is done before boarding.

The restriction applies even if you do not leave the international zone.

Individuals in transit to reach their country of origin who are holders of a travel document to their country of origin and remaining in the international area with no intention to enter the national territory.

If your partnership is recognized as a spousal relationship, and if you are also an EU national and travelling with her, this may also be applicable:

Individuals transiting through France to reach their residence, accompanied by their spouse and children.

Netherlands affirmatively exclude any transit passenger to third countries from its restrictions without necessarily returning to country of residence or origin:

The travel restriction does not apply to the following categories of persons:

Transit passengers who wish to travel via the Netherlands to another third country;

https://www.netherlandsandyou.nl/travel-and-residence/visas-for-the-netherlands/qas-travel-restrictions-for-the-netherlands

Switzerland also exempts transit passengers:

It is possible to stop over at one of the Swiss airports, as long as you do not leave the transit zone of the airport and you can prove that you can continue your journey to your destination country.

https://www.sem.admin.ch/sem/en/home/aktuell/aktuell/faq-einreiseverweigerung.html#Rules%20applicable%20to%20unmarried%20couples

TIMATIC doesn't indicate any extra requirements for same-day airside transfer for Germany and I can't find any authoritative source excluding non-Schengen transit from restriction (although personal hearsay indicates it's possible).

Update:

I asked German Federal Police (excuse my German) at the Frankfurt Airport today:

Mit einem Zwischenstopp in Frankfurt möchte ich von Japan nach Großbritannien reisen.

Ich bin weder EU/britischer-Bürger noch habe ich eine gültige Aufenthaltsgenehmigung. Ist diese Route möglich (durch die internationale Transitzone)?

I would like to travel from Japan to Great Britain with a stopover in Frankfurt.

I am neither an EU / British citizen nor do I have a valid residence permit. Is this route possible (through the international transit zone)?

Reply:

Ja dies ist möglich solang sie den Transit nicht verlassen.

Yes, this is possible as long as you do not leave the transit.

I'll use France for my example since you mentioned that country. Since your partner is a "third-country" citizen, she does in fact need a declaration as stated in the website of the French Consulate General in London:

Anyone travelling to France from abroad is still required to show an official declaration for international travel, in paper or digital format.

This document is required for entry to and transit through French territory as of 6.00 p.m. (Paris time) on Monday 6 April.

Germany has similar, if not more strict, guidelines in place. You can find them here. Briefly, they state the following:

Non-German citizens, including EU and foreign nationals alike, are allowed to enter the country under certain conditions. According to the Interior Ministry, those conditions include:

• transit through Germany to return to one's home country if no other travel connection is possible.(Emphasis is mine)