My $0.02:
Toyota uses the "turn of the bolt" method because proper bolt torque is difficult, even in a lab, where the torque values are initially proven. The idea is that beyond a specified torque value, a specified number of turns (or part of a turn) will stretch the bolt threads, providing a dependable preload. This preload is advantageous because it prevents the bolt "unscrewing" itself due to an unloaded, installed condition. This is the accepted standard of practice in structural engineering for critical bolted connections.
There are several important points to consider when using this method.
First, it was developed for bolts and nuts, not screws, which is what "head bolts" are. The difference is important because nuts have significantly fewer threads (and thus thread length) than a tapped hole does. This means that there is more surface area available to "load" the thread in the tapped hole, resulting in a lower required torque and associated preload. This is a good thing in this application, as it means the chance of doing a good job locking the screw in place is high.
Second, once stretched, a bolt should never be reused because it's impossible to determine how close to the plastic region the material was extended. In practice this means reused head bolts are easier to break. I know there will be several hundred comments from people who've never broken a head bolt (posted or just thought about); they've been lucky.
Third, this applies only to tapped holes which have had screws installed in them and then stretched, chasing the threads actually removes material which is required for proper "grip" on the screw. The reason a head bolt, even a new one, will be hard to install at times is that the internal threads (the hole) have been stretched from their initial cut profile, when the external thread (the head bolt) was installed. Based on my manufacturing experience, I would recommend chasing head bolt threads only if they are damaged, for instance if a head bolt had to be extracted because it was broken. Even then, if it was my engine, I'd sleeve the hole.
As always when measuring the installation torque, you should never stop turning the wrench once you start, because the coefficient of static friction (the force it takes to start the fastener) is, in most metals, 140% of the coefficient of dynamic friction (the force it takes to keep the fastener turning). This is with or without lubrication; the ratio between the two is nearly constant. You can prove this to yourself by watching the scale on your wrench as you turn the fastener.
There's no magic to a torque wrench, it works the same way a fish scale does. A spring of a known size is stretched beyond its free length and because of Hook's Law, we know what the force at that new length will be. The digital ones use a load cell, but the principle is the same. The difference in the quality of a given torque wrench is the initial accuracy and the repeatibility of successive measurements.
If you're really concerned about proper torque, there are many labs and scale suppliers around the country who will certify any measuring tool, for a nominal fee. FWIW, gage labs have to have their tools certified on a recurring basis, because the materials used in the tools relax over time and the "zero point" has to be reset. A Google search turned up these results near you:
Google
An easy way to do this yourself is by comparison. Find a torque wrench you know is good (try a machine shop or manufucturing facility) and use it to tighten a screw. Preferably use one the same size and material you intend to use your wrench on, both the fastener and the material it's going into (I would not use your head for this). Check the static and dynamic torque with it, then with yours. Mark yours so you know what the position of the value you need is on your scale. This is what the certification labs do, although their practice is a little more involved.
To your last point, I like using soapstone welding markers for fasteners. It's oil and heat proof, which means I can use it on parts that I haven't meticulously cleaned, but nonpermanent. Something like this:
Soapstone Marker - Welding Supplies - Grainger Industrial Supply
HTH