Titi and I did some testing tonight:
First Titi was hosting, and I connected to his server, we both had r4141, and the option to reconnect / connect to in process games was active. I was connected form the very start of the game, though. I got a timeout about three minutes into the game. I think Titi also got a timeout then (or maybe a segfault?)
Then I hosted without the join-in-process-games option and Titi connected as a client before the game was started. The game setup was very similar. We started the game, and could play without issues for several minutes.
Then I hosted with the join-in-process-games option and Titi connected as a client before the game was started. The game setup was the same as before. We started the game, and both the server and Titi's client reported timeouts after just one or two minutes of gameplay.
We reproduced this two more times. Apparently this issue only occurs when the join-in-process-games option is active.
We also took network reliability measurements (using "mtr -i5 IP_ADDR" vice versa) but there was no increased latency between us.