"There is clearly a point beyond which running the exercise becomes running the art."
Emphasis is on point as this usage of 'which' is non-conditional.
"There is clearly a point beyond in which running the exercise becomes running the art."
Emphasis on the cause (running the exercise) as which in this case leads to something happening.
The 'in' implies the importance on the second part of the sentence, which can be rewritten as: Running the exercise becomes running the art after a certain point.
Another example would be:
This is the kind of music in which he is interested.
He is interested in this kind of music.
To make it more ambiguous, in which can be replaced by where but by doing this the emphasis/focus is returned to the first half of the statement.
"There is clearly a point beyond where running the exercise becomes running the art."
The focus returns to 'a point'. In which implies that there is a specific point whereas where implies that there is some point, but it is not specific.
This is the box in which he keeps his wallet.
This is the box where he keeps his wallet.
The first example focuses on the wallet. The second one focuses on a box which happens to be where he keeps his wallet.