What does the sign on the bathroom door in a French airplane read when there is someone using it?

For an airline, it's typically just going to either say "Occupied" in English or else use a symbol and avoid words entirely. I don't recall Air France being different in this regard on my flights with them. Some also include the local language and/or other common languages in the region, but almost all signs in passenger cabins will include English at a minimum if they have words at all. For a large, global airline like Air France, where a given jet could be flying to nearly any part of the world on any given day, the signs have to be able to be understood by as wide of an international audience as possible.

This is not so much because of English being the language of aviation, though. That really only applies to pilots and air traffic controllers and, even there, France is something of an exception. French pilots and controllers often speak French to each other on frequency, much to the dismay of everyone else on frequency who lose situational awareness as a result, though this is allowed by ICAO if the pilot agrees.

The real reason for English (or symbols with no words) being used on signs in airliners is that it's the language most likely to be understood by passengers in the vast majority of the world. Airlines (and other travel-related industries) tend to deal with heavily international audiences. It's completely normal for airline flights to have passengers with a dozen or more different native languages, especially on international flights. This is especially true in Europe, where even traveling 300 km will often put you in another country with a different native language. English is the de facto lingua franca of international travel in most of the world, so, when words are used at all on signs, English is usually at least included in order to maximize the number of passengers who will understand the signs. For example, say you have passengers from Germany, Senegal, India, and Brazil traveling to South Korea. The odds are very high that the only language that all of those people will have in common with the South Koreans is English.

I certainly don’t pay much attention to that, but I’m pretty confident they actually use the English wording “occupied”, in red, or just red. Very subjectively I would say it used to be “occupied” and now it’s just red, but I would need to pay more attention.

On the ground in France, if there’s any text (it’s way more likely to be colour-coded: red for occupied and green or white or off for available), it will say “occupé”.

Note that this is for France. Usage may vary a lot in other French speaking countries, I definitely can’t remember what the usage could be in other places such as Senegal or Quebec.

Not quite an answer, but more of a frame challenge:

I think this question hinges on a missunderstanding on how gendered nouns (and following from that: adjectives) work in romance languages. The form of the adjective depends on the thing that is beeing discribed (here the toilet) and not necessarily on the person doing the thing. So what ever the correct word is to indicate an occupied toilet in french (from what I remember of high school french and some of the other answers and comments in this thread I would say: "occupé") it would be the same on the mens and the womens bathroom!

The internal decoration of an aircraft can vary even within one company.

You may see bilingual signs, English-only signs, symbol combined with word(s), or symbol-only signs.

From personal experience, at least some Air France airplanes use the English "Occupied". Air Canada often avoids using words at all and relies on colour and symbol indications, as they are legally obligated to have text signages in both official languages of Canada (English and French), e.g. https://edition.cnn.com/travel/article/air-canada-french-language-lawsuit-trnd/index.html.

Signages with only an adjective in French usually use the masculine form, for example, "FERMÉ" (accents may be omitted in capital letters) is usually used before a closed road, even if the road ("route") is feminine. This is consistent with the agreement with the neutral demonstrative pronoun "ce", but you'll have to ask French SE for the actual reason. It is however not wrong to use feminine alone, although the masculine form is often preferred simply because it needs less space.

However, if the adjective appears with the noun it describes, the gender and number agreement is required, e.g. "ROUTE FERMÉE" or "PORTE FERMÉE". The gender of the occupier is never relevant.