When shooting, you need to **select a valid target**. For this, the difference between the target's order is key. With an Engage Order, an operative is a valid target if it's visible to the attacker. Being In Cover does not prevent targeting - it only provides a cover save when shot.
With a Conceal Order, an operative is only a valid target if **visible and not In Cover**. This is the key benefit of Conceal. It protects you from being targeted at all behind a cover.
Compare the same position with an intervening terrain for two operatives. Only the one in engage order is a valid target.
When shooting, you cannot select an enemy operative if a friendly operative is within its Control Range. This is a Shoot action restriction, not part of the Valid Target definition. Other rules that check for a "valid target" don't include this restriction.