Unclear development plan E+D or II

We have no slope, the property is completely flat, i.e. the basement does not protrude from the ground.

But according to the development plan, you would be allowed to.

Does the basement actually count towards the floor area ratio?

Fully developed floors count towards the floor area ratio. You are making a mistake: you must not call the basement a basement, but a floor. And according to the state building code, there are clear rules as to what makes a floor a fully developed floor. This applies to both attic and basement floors. So study the state building code regarding fully developed floors yourself or ask the architect. However, he also seems somewhat overwhelmed by the legend of the development plan?

Regarding the basement, there is nothing stated about how far above ground I would be allowed to go with it.

Please read again if not understood

Regarding the basement, nothing is mentioned about how far it is allowed to extend above ground.

This is not regulated in the development plan, but in the state building code.
If a basement protrudes on average 1.40 meters above the surface, etc…
That would at least give some logic to your development plan. Unfortunately, in my opinion, that would exclude your house.

Do you have a slope so that it is explicitly stated like that?

Could the house attached in the annex be built there?

Within the height limits and roof slope requirements, yes.

i.e. the knee wall would be above the second upper floor. Can that really be what is meant?

The architect says that a second concrete ceiling would not be possible at level II.

For your information: the floor area ratio is 0.35 and the plot ratio is 0.6.

Knee wall limits have nothing to do with the residential use of an attic and accordingly also apply to attics. You are talking past the "architect" (I assume he is more of a "so-called" one). You probably mean, regardless of the material, a storey ceiling, i.e., that instead of a ridge-open upper floor, there would be an attic added on top. A plot ratio smaller than twice the floor area ratio usually means between the lines that the attic would no longer be suitable for residential expansion.

Regarding the basement, nothing is stated about how far I would be allowed to extend above ground.

This results, on the one hand, from the avoidance of full storeys, since with basement+ground floor+upper floor you would already be at three full storeys; and also indirectly from the reverse calculation of a ridge height requirement; furthermore often (also indirectly) from the reference height for the height requirements. If, for example, the top edge of the finished floor is a maximum of 0.5 m above ground level, the "basement" protrusion is practically limited by that. You can also name the development plan here (without link!, e.g. "Hintertupfing No. 123 in the cool valley"), several forum members can read those documents. I suspect the house profile shown in post #8 was taken from a different development plan (?)

Oh, thank you for the offer. It concerns the following development plan, which I am attaching as a link because the PDF file unfortunately cannot be opened on a smartphone.

It is No. 01
Designation E…-Northwest
3rd overall amendment

Now you can also give the plot number at the same time. By the way, the plan specifies a height limit (at 6m) only for the outbuildings, not for the main buildings, whose ground floor finished floor elevation is, however, determined in accordance with III.5. of the old version (which is stated as still applicable by the 3rd amendment) by mutual agreement between the district office and the municipality. I personally consider this to be challengeable or "indeterminate." Presumably, you can get away with any desired dimension, as long as it does not excessively exceed the customary local framework.