More than 90 days ok with a return ticket?

I will do an unpaid internship in Japan next year and will stay for about 100 days in Japan. I have already checked with the embassy for my country and they said that I don't need a visa - just a tourist visa on arrival and then to extend it, which my country is able to do.
However, I heard that it can cause problems with the airline when boarding the flight to Japan. Does anyone have experience with extending visas and airlines? I don't want to fly with a one-way ticket, I will have a return flight, but it will be after 100 days while the visa I get on arrival will only be 90. Could there be problems or do I need to check with the airlines before booking the flight?

Embassy for your country, you say? Please check with the Embassy of Japan in your country about the (1) unpaid internship not requiring a visa and (2) whether you can extend the resident status once youfve entered Japan. (Hasnft there been some info that unpaid internship does not require a visa, but only up till 90 days?)
Airlines: is there any way you can purchase a return ticket with a changeable date, or the return date open?

Be aware of the procedures/requirements.

https://www.mofa.go.jp/j_info/visit/visa/short/novisa.html

Germany([Note7])
([Note7]) For nationals of those countries with visa exemptions permitting stays of up to 6 months under the bilateral visa exemption arrangements, those who wish to stay in Japan for more than 90 days are required to apply for an extension of the period of stay to the Ministry of Justice (Regional Immigration Bureau) before the period of permitted stay is to expire.

Any unpaid activity (that doesn't otherwise violate Japanese law) is fine on Temporary Visitor status (Less than 90 days) More than 90 days you need to have the "Cultural Activities" visa .

Please check again before you enter Japan and violate the conditions, which may bring some issues.

Thank you for the answers, I think I didn't clarify enough. My unpaid internship will last 89 days, but obviously I need some days before and after to settle in and move out of the country again. So I need to extend my visa and hopefully don't have issues so I stay about 100 days in total.
My concern is actually that this might cause questions or issues at the airport due to my return flight being later than 90 days. So I wondered if it would be better to book a flight with a changeable date or if it would be fine to set the return flight after 100 days when I come to Japan.

To me, as the total duration of you stay, of which internship IS the main objective, exceeds 90 days, it might be considered a borderline case even in terms of immigration.

OK, about the airline. The airline wants to make sure that all their passengers are OK to stay for the duration of stay they plan to, otherwise, should the passengers get turned away upon arrival, it would be their responsibility to take you back to where you came from on the next flight

Speaking from my experience, I believe it would be better to have the return flight either open (meaning no date booked at all, but the return ticket is valid for the date you actually need it), or book it under 90 days on a changeable ticket.

I say this because (though this was years ago) I traveled back to Japan with my (now) spouse, back then not yet married, hefs from the same country you are, he tried to enter Japan stating g180 daysh as duration and having a ticket (fortunately changeable). And upon arrival in Japan he got pulled over and was questioned, and was told bluntly (when he pressed that Germans should be able to extend it to 180 days) that yes that was supposed to be reciprocal, but in practice it was not guaranteed that he would get the extension.
On another occasion, he did have difficulty convincing an airline staff upon leaving another country which hefd visited out of Japan that it was OK for him to board heading to Japan, though at that time he did have a different resident status that allowed him to stay longer.

Soc seeing that what you are currently eligible for is up to 90 days, Ifd suggest get a return ticket with a date under 90 days (changeable), or get a completely open ticket.
Also as you will be leaving your work place one day to go to immigration bureau to do the extension application, be sure your employer knows of this.
(A regular poster here, but staying anonymous on this thread.)