DRCs for component to component clearances depend on what information Altium has to work with.
For example in the first screen shot below you can see there is DRC clearance error for U1000.
When a part is selected in the 3D view the perimeter of the part and it's primitives are defined.
The part perimeter includes the silkscreen (Overlay) layer when a component body is not included in the footprint.
In the example below the pin 1 character on the Top Overlay has defined the lower extent for the component (U1000).
Altium uses extruded component bodies and step models if they are available when checking for component clearances.
After adding an extruded 3D body to U1000 and running the DRC check again the design passes the component to component clearance check.
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