Agree about the pretend pilot removal and go for pure telepresence. I'd remove the cockpit altogether as a human presence demands so many additional tech I find it unlikely it would be there unless always piloted by a human.
I would like the telepresence distance to be higher though.
On player across-the-galaxy telepresence; FD never tried to find scientific explanation as it is clear there can't be any. It was added for fun gameplay reasons and I have no problems with it, it is a game afterall. But the differences it brings (additional pip, SLF...) should definitely be removed.
There's plenty of reasons why the ships would have a cockpit of some kind though, even if
we ourselves never make use of it. Sometimes there might be interference, other times the fighters might need to operate inside shielded installations, they might need to operate beyond the reach of an appropriate telepresence array. It could even just be simple cost, as (until the multicrew retcon) those telepresence suites were large and expensive things such that even a mighty class 7 hangar can only fit a single one. It would simplify design a lot to have a hybrid design that can be operated remotely or by hand depending on circumstance rather than catering directly towards both markets with specialised products.
FD did try to find an explanation for across-the-galaxy communications, the problem is that it basically invalidated 80% of the existing setting as it meant that zero-latency, high bandwidth FTL communications because accessible for everyone. As I pointed out, they could have had a system where multicrew involves a remote player possessing an existing crew member without any changes to the lore. No interstellar communications necessary, the crew member is on your ship already. No need for travel delays, because the player's actual CMDR isn't there, they are just out-of-game controlling an existing crew member. No lore breaking, no real gameplay concessions (except the host ship requiring a crew member present, which an SLF equipped ship should probably have anyway), just a simple system that merges both the existing NPC crew and multicrew.