When you max out the search skill and it AOE searches, you don't get XP from it. You do when it happen with the present.
Fixed in 1.5.0
It's the same with the friendly Earthling that you can pay to follow you & shake the surrounding environment. No XP. I find it disincentivizes using the NPC.
It's interesting you mention the Come Out present acts differently. Consistency would be ideal. (I myself have never noticed this, good spot!)
In your case, as a player, I would seek out a UFO to reduce some skill points - if you feel the XP gain is worth the tradeoff. Another alternative is to use more coin meters & enter the HFZ for XP.