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Description
Tested using MeshLab version v2025.07, on MacOS arm64, M1.
When trying to open a 3MF file, MeshLab offers the "Transform vertices instead of using transformation matrix" checkbox in the pre-open dialog. I assumed that this option only changes how the object is represented internally, and would not (significantly) affect how the object is displayed.
However, it seems that for certain 3MF files, checking the checkbox greatly alters the displayed objects. For example, using the test file multiple_cylinders.3mf from the 3MF example repository, this is the object displayed without checking the checkbox:

And this is the object displayed with the checkbox checked:

Two of the cylinders seem to be transformed incorrectly. Here are the 2 broken cylinders from a different angle, after hiding the other 4 correct cylinders:

The same issue appears on other files such as cube_gears.3mf, where all meshes except the first one are shrunk by a lot: