It is very common for these parts to align as you show in your pictures. Some builders have had them replaced and others, like myself, have had to buy new parts. I got lucky and my second set aligned much better. I am on page 38-21 and just starting to see the alignment with the roll bar and itís not bad. Thereís a lot going on at that interface so the likely hood of the window/canopy lining up perfectly are quite low. I plan to use non metallic washers under the window or canopy to get it aligned where I like it. Side note, use the C-01405D under this joint and not its little brother C-01404A.
This was the original, replacement was much better.