Realtalk: let's do Actual Elite Lore TM answers:
So if my crew members are just holograms and they have full control over my fighters, why does my NPC Pilot have to die when my ship explodes, and why must they be present on my ship at all if they could just holo-hop from the other end of the galaxy?
1) Your NPC pilot is not a member of the Pilot's Federation and therefore is not allowed to telepresence into ships in a command position. He's physically on board the ship. He is allowed to telepresence locally.
Why can't I just holo-hop into my ship so I can deactivate my life support for more power?
2) Pilot's Federation regulations state the Helmsman must be physically present on the ship.
If no lag real-time galaxywide 2-way comms are a thing, what's the point in my cmdr even getting into his cockpit if he can just poof anywhere in the galaxy where there's a chair?
3) Again, the Pilot's Federation does not allow ships capable of independent flight to be piloted via telepresence.
I feel like this holo-telepresence magic is just a bad explanation for what should have been "it's a game, and they join your instance so you can play with friends".
The game takes place in a setting where you, the CMDR, have received a Pilot's Federation License that makes you one of the most powerful people in the galaxy from your first log on at Trevithik Dock. The Pilot's Federation controls all ship computers instantly, it tracks all actions via these computers and it is de facto the most powerful organization in the galaxy because no intersystem travel is possible without use of ships that must conform to Pilot's Federation standards. The reason you can't jump to systems without permits is because your ship computer does not allow you, but because of the GalNet, an intergalactic, instant communication system, you receive permission when you meet requirements. The same goes for ranking up, for example. All of this only works because the Pilot's Federation can, via GalNet, control and update all ship computers instantly. This is how wanted status propagates, this is how your reputation with factions works, this is why ships flag as legal or illegal targets. Everything in the entire world of Elite is, canonically, dependent on the Pilot's Federation's possession and control over a network of information that works instantly. When someone turns in data to Universal Cartographics, that data propagates instantly to every ship computer in the galaxy.
Canonically.
In this setting, one of the most popular religions is for people who can afford it to literally plug themselves into simulated realities where they enjoy a life of bliss receiving spiritual teachings from their SimGuru. This is an established piece of the canon which was present in game through Patel and so on.
In this setting, canonically, both instant communication of information
and telepresence and fully immersive virtual reality are not only conceits to explain gameplay, they are
fundamental basic realities of the setting.
All of the limitations you're talking about are the same as the limitations of why CMDRs cannot land on populated worlds: the Pilot's Federation does not allow it.
Why can I telepresence as a gunner but not as a Helmsman? The Pilot's Federation does not allow it.
Why can't my NPC (non Pilot's Federation guy) telepresence to my ship? The Pilot's Federation does not allow it.
If we're going to have a kvetch about the lore, we can do that, but saying "it's not lore consistent" when it 100% entirely is is ridiculous. Let alone the fact that lore should never, ever get in the way of good, fun gameplay.