Prepositions – Working In, For, or At?

The preposition within has nothing to do with the ordinary sense of the preposition with = “accompanying, alongside, by means of, etc.”. Within means “inside” in spatial, temporal and figurative senses.

The hoard was discovered deep within the mound.
You must respond to this communication within thirty days.
They are within their rights in refusing to be interviewed.

Consequently, within is not a valid translation of German in in this context. However, English does support both German uses: you may use either with for mit or in for in.

With this option ...
In this option ...

• HISTORICAL NOTE, for those who wonder why the compound with + in has this meaning:

  Old English wið (cognate with German wider) originally meant “against, by, back from”, and the modern sense of with was expressed by mid (cognate with German mit). In the later part of the Old English period, however, northeast England was occupied and to some extent settled by speakers of Old Norse dialects, and over the next centuries (down into the Middle English period) many Old Norse words replaced the corresponding Old English words. For instance, they and are are of ON origin. Old Norse við, a cognate of with and wider, had approximately the sense of mid and mit, and under its influence, with shifted to the modern sense. However, the old sense lingered in established compounds such as withstand (stand against), withhold (hold from), withdraw (draw away from)—and within (against or by the inside).

I am working for a project in my company

This makes it sound like the project is your employer, or somehwat like that you are attempting to win a project for your company.

I am working on a project in my company

This is idiomatic.

You wouldn't work at a project unless the project was a place.

It's easiest if you just think of work on X as a phrasal verb that means "to perform work upon X and/or try to advance X to a state of completion."