"According to the requirements for KfW40 and the (preliminary) information from our structural engineer, we have increased the exterior walls from the original width of 42.5 cm to now 49 cm, and additionally planned interior walls on the ground floor according to structural engineering with b = 17.5 cm. This leads to a slight loss of actual living space, as well as small shifts in the interior walls according to structural engineering. However, this is absolutely necessary.
Well, then everything is clear!
We have – free of charge – increased the width of the captain’s gable from the original width of 3.49 m to now b = 3.74 m. The reason for this is that the two supports on the ground floor must be about 55 cm wide (structurally required). However, in order not to make the entrance area of the house narrow and small, while at the same time the supports are very massive, and to visually emphasize the supports nicely, we decided to enlarge them."
Clearly no one is trying to take advantage of you. By the way, your general contractor plans precisely in the eight-centimeter grid, so no brick cutting / botched pockets. For that reason alone, many builders will envy you – at least those who go unprotected to a general contractor.
So what I actually wanted to get at here: Should I now open a can of worms with the general contractor or is this "just the way it is" and something I have to live with now?
As I already said, there is no can of worms to open and this is not a case of "it’s just the way it is." You have gotten a model general contractor, and your mistake of not telling him to make an adjustment in wall thickness without reducing living space (i.e., outward) can still be fixed with a three-line email. That will cost him a few mouse clicks, then you will have your house 13 cm wider and deeper, and you will pay the price for that.