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Well, protocols do state that if an emergency goes down, the commanding officer has to be notified, even if they are off-duty or asleep.
 
Well, yeah. What else are they supposed to do, ignore it until morning?

"Sir, priority one distress signal coming in from a civilian freighter on our side of the Neutral Zone."
"Can they hold out until morning when the Captain wakes up?"
Those freighter captains are so inconsiderate of when they schedule their emergencies.
 
Trek certainly has space for logical landing parties. It even acknowledges it

The Ultimate Computer (via chakoteya.net) said:
M5: General survey party requires direction of science officer. Astrobiologist Phillips has surveyed twenty nine biologically similar planets. Geologist Carstairs served on merchant marine freighters in this area. Once visited planet on geology survey for mining company.
DAYSTROM: Why were the Captain and the Chief Medical Officer not included in recommendation?
M5: Non-essential personnel.

However that episode also gives us the reason that Kirk leads the party

There are certain things men must do to remain men

And Return To Tomorrow

Risk. Risk is our business. That's what the starship is all about

Does it make logical sense? No idea, we have no idea what the optimal operational procedures for a ship (military, civilian, or mixed) to deal with interstellar exploration. We can infer it will be similar to the european exploration of the new world in the ages of discovery/sail, and certainly historical record claims that Captain Cook led the landing party into Botany Bay, Columbus's diary claimed he was the first out of the landing boat, etc.

Whether taking the full Kirk approach was sensible, but other captains tend to either send the XO or leave them behind, it's rare to have a landing party / away team with both captain and first officer, outside of Kirk.
 
Does it make logical sense? No idea, we have no idea what the optimal operational procedures for a ship (military, civilian, or mixed) to deal with interstellar exploration.
Logically, the ships would carry specialized teams whose job would be to go down to the planets and do the exploration/surveying sort of thing, like the SG teams in the Stargate franchise. Indeed, I would imagine a Galaxy class ship carrying ten such teams with specialists from the ship's crew going down as needed.
 
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