Overwriting UV map or vertex color data in Geometry nodes will move the
layers to another CustomData channel, and as such, will make attribute
lookup fail from the UVMap and Vertex Color nodes in EEVEE as the
CustomDataType will also be modified (i.e. no longer CD_MTFACE or
CD_MCOL).
As discussed in T93179, the solution is to use CD_PROP_AUTO_FROM_NAME
so that the render engine is able to find the attributes. This also makes
EEVEE emulate Cycles behaviour in this regard.
Apparently it is enough to just modify the CustomDataType parameter in
calls to GPU_attribute, as the rest of the draw code is already
handling CD_PROP_AUTO_FROM_NAME cases and already properly alias
attribute names. CD_MTFACE and CD_MCOL may still be used for default
layers (with no names) so their handling in the draw code was not
removed.
Demo files downloaded from blender.org, as well as some selected
production files from the Blender Cloud, are still rendering fine.
However, this change might introduce some rendering issues due to name
collision between UV maps and Vertex colors.