It isn't really that weird, these are androids who are just learning to be more human and they have yet to learn the difference between a complete stranger walking in on a naked girl and lover or other person close enough to not be surprised or too embarrassed walking in on a naked girl. They only know one way as being the human way to react, which is to stop everything and cover up when a guy walks in on them, no matter who it is.
There IS a way to stop this, however, no mod required. Just don't let their humanity get too high, above 99 I believe, which means they won't learn this one and only way to react to being walked in on, however, this also means they just won't react to it. They will completely ignore your presence and continue showering like they were assigned the task with no free will of their own to react any other way than to carry out that task.
Plus there's this, we're talking about a Japanese company who originally designed this game for Japanese players. If the androids started reacting like they knew and were okay with it, there would be people on the Japanese side of the player base with the same issue, that they aren't acting naturally. Remember that acting naturally is defined by the culture, so what is natural in Japan may not be natural in other countries as well as the reverse.