It seems like they do separate damage already in some way, but updates don't specify one or the other.
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They do separate damage as in overall because players in pvp only have 200 total HP (counting shields) so shotguns do a base damage. But the drop off is now 20% less in pvp and pve... So they made an already weak pve weapon even weaker.
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In higher difficulties shotguns definitely are not the way to go....everything has an advantage over you and tour only tools are range and trying to isolate enemies one at a time.