What you are saying is that the whole theory of aftermarket addons and increasing power is a conspiracy. Think about what you are saying.... If it were, would people still be spending money on increasing the power output of their engines?
And if there is more air in the cylinder then that is a good thing. Increasing Volumetric Efficiency (remember, efficient is good) is the whole goal of modifying an engine. As we all know, tuning an engine is all about balancing, giving up something for more of something else. Simply put, you cant have it all and a free lunch too. The ford engineers designed the cam to give the broadest power curve in the area where most truck drivers need it. Thats down low. Unfortunately, we have to give something up for a broad torque curve....in this case that happens to be airflow. Short duration and low lift cams that make great power off idle dont flow very good, but offer a broad torque curve for most street drivers. Dont expect it to make power above 4500 rpms. Wonder why the ports are small? Now its all starting to come together. More velocity with smaller ports, small cam, great off idle power, but not very high airflow. Thats exactly what it delivers and it works for millions of people, but increasing the VE of the engine is a good thing that wont hurt it at all, but infact will help it. However, a K&N is not going to change much in the department of VE. Why you ask, well, the airfilter is not the bottle neck of the system of these engine. (remember the small cam and small ports). While a K&N might give the engine quicker throttle response or might make 5 hp up top at say 4500rpm where VE has dropped near 70%, its not really changing much. The ecu has no problem adding fuel where needed, thats whats so great about fuel injection. It has a MAF to meter the air, and fuel trims to fine tune the mixture. You dont have to do a thing.
You using the term "compression ratio" is misguiding. Compression ratio is static in that it doesnt change. It is all dependent upon piston dome design, combustion chamber size, and head gasket thickness. What changes is cylinder pressure (dynamic compression) by the cams timing events and engines instantaneous rpm. This is how people can run 12.5 and higher compression pistons in vehicles. The late closing of the intake valve helps to bleed some compression off. A high duration cam actually requires a higher compression ratio in order to idle. Bleeding off too much causes a low compression stroke and therefore inefficient combustion not allowing the motor to idle. Let me get back to my point... Ford doesnt build these things close to their maximum compression ratio, infact, im not even sure where your trying to go with that. Most 90s engines have an average CR of 9:1 (4.0 OHV is 9:1), however, today its closer to 10:1 (4.0 SOHC is 9.7). Wonder why, efficiency. Higher CR gives better throttle response, more power, better efficiency, and most important to auto manufacturers, better gas mileage. Ford increased the CR but they still run fine, in fact, much better than prior engines. Your right in the fact that higher cylinder pressure increases cylinder temps (measured by EGT), and therefore can cause detonation, but not by a K&N. Not gonna happen. If we were talking about forced induction, yes, more air forced into the combustion chamber will raise cylinder pressure and might detonate. Higher octane would remedy this. But more importantly, its not the increase in cylinder pressure that induces knock, but rather the increase in cylinder temperature (compressed air from turbo/blower is hot air). Add some meth to cool it down and cylinder pressure wont mean a thing.
Welcome Visitor! Please take a few seconds and 
