I’ve found this post and tried the suggestions in the reply, it didn’t work for me.
I had shapes that need to have a stroke added behind them, and then the original shape removed so only the out-side aligned stroke remains, visually suggesting the inner shape but actually having it removed. The same problem occurred—-when converting the stroke to an outline, it acted as if it was center–aligned—thus cutting into the main shape visually. But I wanted all of the original shape to be seen visually, with the stroke turned into an “outlined” shape outside of it.
I went about painstakingly drawing over the stroke which aligned to the outside and making a new ‘shape’ based on it, using that new shape as the bottom one for the “cut-out”pathfinder tool.
But then realized a center-aligned stroke with a 2 point stroke weight looks the same as an outside-aligned stroke with a 1 point thickness.
I was then able to:
1) copy/paste in place the shape (with shape and stroke) directly over the top of itself, then remove the stroke on that duplicate
2) change the original outside-aligned stroke shape to center-aligned, double the stroke weight, and convert stroke to shape
3) use the pathfinder tool to cut the top shape (no stroke) out of the bottom shape (with outlined stroke just converted to a shape).
4) visual result is an outline around my shape with the desired width not cut into the shape itself, and the original stroke now a shape of it’s own.
Whew, hope that makes sense. Good luck to others with the issue.