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1. As the spark plugs wear over time they loose there integrity and the ability to burn all the fuel in the cylinders. This is why the problem is not showing up till now.
2. You are correct in your thinking almost. The engine can not control how much oxygen it takes in. Please do not think I am saying you do not know what you are saying. Basic physics tells us the colder the object the denser it is. The colder the air the smaller the oxygen is, thus the more oxygen you get for the same amount of volume of hot air "same for the fuel". If you drive the car the exact same way hot or cold out side, you will use more fuel in the colder days then the hotter days.
3. On colder days the weaker spark will be able to burn more of the air and fuel due to the added amount of air and fuel the engine has taken in. On hotter days there is less air and fuel taken in so the spark has to burn stronger to be able to create a better combustion in the cylinders.
4. If the spark plugs are burning the fuel in all cylinders the same then no the engine will not miss, shake, or set a trouble code in the pcm. The pcm only detects if a cylinder is off balance from the rest of the cylinders.
I hope you understand I am not a physicists, I am a auto technician. I hope I have made it easy for you to understand and I am sorry if I am not succeeding. Have the spark plugs replaced and see what happens with your next two tanks of fuel. Make sure to use only factor recommended spark plugs. Most tune up places do not use factory replacement plugs," they use the cheapest thing that will make your engine run". At least that is what most do here in the states. Second of all, using the cruse control will use more fuel then if you where to control your speed. Cruise control does not hold the speed at a set speed, It will accelerate to get you up to speed then will back off till you drop to a certain point then accelerate again to bring you back up to speed. If you control the speed your foot will hold the throttle at a more constant speed and use less fuel.
It appears that Jamie is finished working with you based on his last post.
I don't get the pleasure of working on too many of the speed vehicles and let me say that I envy you being a speed owner. Now, that out of the way... down to the nitty gritty :)
One of the big problem areas with the 3 is the purge valve. I lost count how many of these thing I had to change. Many times they will not set a code and you may not notice a running condition especially in the cold. When they fail they suck fuel vapors into the engine all the time. I have also seen them suck raw fuel in! The engine is pretty good at burning the fuel/vapors that are sucked in but in never seems to give increased power. The symptom more experienced is a lag on initial acceleration. I figure this happens because the engine is temporarily flooded. Based on your details you would be less likely to notice this condition since you do a highway drive everyday.
You can do a superficial test of the purge valve by removing it from the 3 and trying to blow through it. If you can blow through it then it is stuck open and needs to be replaced. The problem with this test is that they don't usually stick open and stay open so when you test it, it may be working properly. If you haven't ever replaced the purge valve/solenoid then it is highly likely it has failed and is creating an overly rich condition.
I read through the scangauge manual online about the correction factor. It seems that this should only need to be set one time in the beginning. I would start by resetting the scangauge and performing the correction procedure for the tank fillup.
Also, I would trust the onboard computer more because it uses information directly from the PCM to gather vehicle speed and amount of fuel used to calculate the average consumption. If I were you I would be comparing the onboard computer values for the time periods in question. The scangauge is subject to too much user error and accuracy problems.
Another thing when calculating the average consumption. I am not sure how the computer calculates for fuel used when not moving. This is after all consumption of fuel! It could be that your hand based calculations (distance traveled/fuel used) is showing a discrepancy with the onboard computer. This may be because the onboard computer only calculates while the vehicle is being driven. Again I don't know for sure the calculation methods but this is something to think about.