Even Beethoven's pieces hardly have any fingering marks at all. What you should think about this, then, is that the strict words you have been told about fingering, and the problems you have had in learning it, are just what people have come up with later, saying this style or that style of fingering. Another problem you are going to face when playing music is articulation, which means the way of dividing up a piece musically. These divisions have something to do with fingering. So you can understand that articulation has something to do with fingering.
Articulation thus is related to fingering.
If you understand that, then it gets interesting. That means that the joy you get from playing Bach is sort of a professional joy, I think. Some people don't think that way, probably. However, if you decipher it that way, it resolves the problem of articulation. However, since you are in the process of learning, we use the thumb and the little finger, and cross over and go under, etc.