Hi Tuk,
Apologies for the slow reply – for some reason the notification for this post went to my spam folder and I just saw it now.
A 1 cm difference isn’t a big deal (it’s about 1% of the overall length of the seam) and it won’t make a noticeable difference in the finished packraft, but how to accommodate it depends a bit on the adjacent tubes (#2 and #4). You mentioned a photo that shows tube 2, but I don’t see that one (it looks like you accidentally uploaded a different photo twice). Can you send me that other photo? That will help me decide the best way to proceed.
If you’ve already gone ahead and started sealing things together, don’t worry about it. As long as the tube corners are aligned with each other, the placement relative to the slits doesn’t actually matter.
Thanks