This is a common problem affecting app using its own NE implementation (instead of using iOS's built-in VPN clients), e.g. commonly seen with VPN/PacketTunnelProviders.
https://developer.apple.com/forums/thread/99042
Apple doesn't appear to be interested in fixing this, since they did nothing with the bug reported in that discussion thread. There must be some way to get Apple to do something about this. The battery impact is likely calculated based on the estimated cpu and radio usage for the traffic performed by the NE, so a simple thing for them would be to deduct the "inside" traffic being performed by apps going thru the NE from the "outside" traffic blamed on the NE when calculating battery usage.