If tube 1 fits nicely between tube 2 and the center slit then I would locate the tubes as you have them in the pictures without modifying anything, but if tube 1 doesn’t fit, then I would trim the corner in this picture to make tube 1 fit.
It looks like it extends about 5 mm past the slit, so I would trim off 5 mm at the corner and gradually taper the trim so that it merges with the existing edge after about 20-30 cm (8-12″). That will not make any noticeable difference in the shape of the packraft.
Alternatively, you could trim the tube 3 in the same way. Note, however, that unless you are diligent about tacking the fabric in place before you weld it fully to the floor then you can expect the tube fabric to shrink a small amount as you weld, so if you trim everything before you begin welding then you could find that the parts end up smaller than you anticipated. That is why it is important to tack the fabric in place with the edge of your iron before welding it with the flat part of the iron.
Does that all make sense?