with the landing gear there's mechanical backups. the pilot can (destructively) manually drop the gear if there's a failure. same with other backups: on a non-fly by wire aircraft, the pilot can physically move the control surfaces with enough force. even Airbus has a limited mechanical backup (which has been used a couple times! like when all three avionics controllers disagreed and tripped offline.) likewise, even when there's a total loss of power, the pilot can windmill the engines to start. and since any loss of communication dooms the aircraft, it needs to be extraordinarily reliable - and I'm not sure that level of reliability is physically possible, because the underlying communications links (even ACARS) aren't rated for it, nor are the backbone routers of the internet.
finally, I think it is human nature that remote pilots will become complacent if their own lives are not at stake, like their passengers'.
I'm sure it's fascinating research, and may have a place for cargo/repositioning flights, but I can't see that such a scheme could be made reliable enough to risk human lives.
specifically this is how QUANTUMINSERT worked (from the Snowden leaks.) also China used the same technique, injecting malicious JS through the GFW to get bystanders to DDoS github, in a much more obvious and indiscriminate way.
nobody here is remotely likely to be targeted by NSA, of course, but you can actually do such attacks on a budget if you compromise any router in the chain. combined with a BGP hijack it's not far out of reach for even a ransomware gang to pull something like that these days.