Looks correct to me. Have you loosened all screws on both rows and tried to to slide the modules into place? There’s a little wiggle room in the tapped strips and the module mounting holes that doesn’t settle into place until the modules are screwed down tightly, so it’s important to do initial installation with them loosened. The sheet metal boats are precision laser cut, so rail positions shouldn’t be a factor. It’s meant to be a tight fit, and the faceplates themselves add to the structural rigidity of the finished enclosure, so if you’ve tightened modules down on one row before installing them in the opposite row, I’d expect things not seating right.
In the photo above it looks like the modules in the upper row’s bottom holes are off by about 1.0mm - 1.5mm, but the Cortex module below it looks like its top faceplate isn’t flush with the top of the rail.
If there’s a little tension on the aluminum faceplates at first then that’s perfectly okay – they’re a structural piece made of 2mm aluminum (a bit thicker than typical EuroRack faceplates.) Generally once you have modules aligned and screwed down then the rest of them you install will fall right into place.
And to be clear, the inner rails look OK from your photos. Can you confirm both of the two outer rails/struts do not show exposed thread/channel? (they should be smooth all the way across)