Yes this will often happen when setting the HST's in block designs. It depends on the block design. I still prefer to press to the dark, then if the setting has the HST's turned in such as way that they won't nest, then I have to decide what to do.
Sometimes I roll the seam allowance over so they will nest. That will cause the other end of the seam to now be facing the light. If this is not a problem with shadowing or other piecing seams to follow, then I do that. I do repress the HST. This preserves the ditch.
Sometimes I pin the two pieces well, and sew the seam without them nesting. This causes a bit more bulk but also preserves the ditch.
Sometimes I repress the seam allowance open on the HST's so there is no nesting and no ditch. I do this for very small patchwork to reduce bulk.
Sometimes, I will flip the seam allowance by hand, nest and sew the seam, and keep the other end still facing the dark. This does create a twist along the middle of the seam area, which I then force into submission with lots of steam and pressing! This option works well when I know I will be quilting the quilt with an allover or pantograph pattern. If the quilt will be having custom quilting with Stitch in the Ditch, then this is not a good option because the ditch will keep flipping back and forth.
Some piecers (not me) twist the seam allowance to nest it, then clip it in the middle so half lays one way, half the other, way but both are now flat.
You might want to make a few test blocks to see which method you prefer the look of. And keep in mind the desired quilting (SID?) too.
Sorry if this is not helpful -- there really is no perfect completely right answer to this. Just choose the best option for the quilt you are making.