@mdjurfeldt Because one can select the molecule (Ctrl + A) and move it on the canvas (after Ctrl + 6, or toggle on the hand symbol), including somewhat closer to the optional reference axes: does the accidental superposition still occur after the selection of the molecule, and view → center?
Does the superposition equally occur for the export to wrl/vrml (mentioned here and here)?
For a few small molecules (lutidine, diethylether, etc.), running the Linux appimage 1.100.0 from a thumb drive in Debian 13/trixie, I didn’t observe the problem your report. However, was your structure a much larger one (possibly a protein read by import from PDB)?