My guess is: The Targeting System works like a radar and scans longest-ago scanned chunk. And chunks that are in active radar range are always up to date so they get never scaned.
You can remove the radar at that one outpost and replace it with an auto-targeter, which should clear out the bases nearby. Once they're cleared, you can put the regular radar back.
Alternatively, you can clear the bases manually by walking there yourself or using the Satellite Uplink Station.
Is there a change in the behavior? Your mod is really great. However, it would be nice to auto target enemy bases in radar range. Maybe with a button to scan all sectors or so. Thanks for reading and this excellent mod.