It was designed to be aligned up.
Did you notice if it was the same before you removed the undertray? If it wasn't, it’s due to the refitting process.
Is there any ‘give’ in the duct so that you can move it slightly into position?
If it was the same before you removed the undertray and you haven’t had any issues then I wouldn’t be too concerned about it.
I recently posted the undertray (Radiator Splash Shield) removal and installation TOPIx file here....
https://www.ftypeforums.co.uk/viewtopic.php?p=68161#p68161