Is it just buggy me or Adobe isn't thinking it's a necessary privilege?
I don't think it's a bug. It might be inconvenient but it's just that once you have made a Shaper Group object, it doesn't allow you to change the stroke alignment. You could of course expand the shape made with the Shaper tool, then apply a different stroke alignment.
In fact, using the Shaper tool on shapes with strokes aligned to anything but centre, automatically switches the alignment to centre.