don't understand what makes a warm charging system produce a greater output than a cold one.That is, assuming it is a greater output to begin with.
Besides the fact that the voltage regulator setting is designed to drift with temperature changes I agree that it's probably just the battery recovering from the drain of the starter and while the battery is drawing some current the charge voltage will be lower and so the light will come on. Without getting into a complex explanation of why this should be it's basically down to ohms law and a small voltage drop across the battery due to it's internal resistance.
In fact what you have observed is interesting because it's a very good demonstration of the fact that if you are going to judge the charging circuit by measuring the voltage at 3000 revs the battery must truly be 100 % fully charged to get an accurate assessment.
My own observations of making changes to the voltage regulator setting are that it does change the behaviour of the charge lamp so to some limited degree you can judge the health of the system by the lights behaviour. For example when I had the voltage regulator set a fair bit too high something like 14.6 volts then the light went out and stayed out even at ridiculously low idle speeds of say 700- 800 RPM.
Lowering the voltage setting to the nominal 14 volts will bring on the charge light at those revs.
I'm currently running with a setting of 14.3 volts which as high as you should safely go with a wet cell battery. My charge light now goes out and stays out at a 1000 RPM idle.
Bear in mind that an electronic ignition bike particularly a US version will not exhibit the same charge light behaviour as mine due to substantially more load from the ignition system and headlight. The extra current draw is not balanced by the charging system until higher revs are reached and so the light stays on at low idle speeds.
For me that says US electronic ignition bikes should have the highest possible safe voltage regulator setting and while plenty of owners seem to spend very large sums on upgrading the alternator the very first thing I would do is fit a "high output" or better still an adjustable voltage regulator.