If I understand you, I think the answer is no.
When importing an object, Giles creates a list of materials used, but any lightmap Giles generates uses another UV map per material - it does not take existing UV into account when packing a lightmap.
However the author has hinted that a new version is coming soon and it may have the ability you're wanting.
When importing an object, Giles creates a list of materials used, but any lightmap Giles generates uses another UV map per material - it does not take existing UV into account when packing a lightmap.
However the author has hinted that a new version is coming soon and it may have the ability you're wanting.