I always figured that all of those little gaps/etc. were due to a couple factors:
1.) the aircraft are constantly being upgraded/modified, so even if you designed the aircraft to be gap-free initially, there will inevitably be changes that introduce them. The cockpit itself is basically a frame with racks that hold all of the avionics, seat, etc.
2.) in conjunction with the above, ease of maintenance was somewhat important, so they tried to leave at least a little room to maneuver in the cockpit where possible (though there were plenty of places which were a nightmare to work regardless), but that comes at the cost of introducing areas where things can fall.
3.) some components have to be regularly removed and worked on outside the aircraft, or must be free of obstruction during flight, e.g. the ejection seat. So you end up with plenty of gaps where things can fall.
A general engineering design principle is that things degrade smoothly so that there aren't abrupt changes in performance.
The aircraft controls should be protected such that foreign objects should have a low likelihood of jamming them. That there aren't things preventing someone from clearing any blockages and there aren't places where they could lever themselves in.
My car has a design flaw with respect to the floor mats and the accelerator pedal (its not a Toyota). Between how the lever arm and the pedal surface itself are design and the aftermarket floor mat, if the mat slides forward it can jam the accelerator down. These are the deep groove mats for catching mud and water. The designers didn't think of this, if the pivot point for the pedal was further up the firewall. The pedal also has a hard square edge. Both of those things are in general a design flaw for pedals. The NHTSA (National Highway Transportation Safety Administration) should and maybe they have (my car is old) the design of the pedal linkage and the shape of the pedal to reduce this kind of risk. The hooks for securing floor mats should also be standardized to help keep them in place.
The hard mount points for child seats are a great positive example of this.
You're comparing child seats built for the greatest common denominator to high tech war machines that were built on the principle of "kill or be killed" for the best funded and most advanced armed forces on Earth. Every kilo of paneling is another kilo that slows down the aircraft, reduces its range, and changes its balance/maneuverability.
Aircraft technicians are just expected not to drop pens and other crap in cockpits and engines on a regular basis. It's a completely different operational context.
Do better is not the solution. And we aren’t talking about aircraft technicians, I am talking about making designs robust against small parts. It could be a pen, a shoe, a piece of glass or a body part.
You make it sound like paneling, which I didn’t mention, some how has the capability to unbalance an aircraft.
We are talking about different things.
