Thanks for the feedback. I reiterate somehow rewarding and adding questions 
1) Assume a PA with an output impedance of only 5 ohm delivering 100 watts to a 50 ohm antenna through a 50 ohm coax. Will the SWR/Power meter indicate 100 watts?
That is correct. However, if your SWR isn't 1, some meters will show Forward power which is the combination your output power and the reflected power. If that is the case, you would need to subtract the reflected power to get back to your 100 watts of output power.
2) Assume a PA with an output impedance of 500 ohm delivering 100 watts to a 50 ohm antenna through a 50 ohm coax. Will the SWR/Power meter indicate 100 watts?
Yes with the same caveat as #1.
3) In short, may I always trust a power meter when the feed line and the antenna are matched to 50 ohm notwithstanding the impedance of the PA output may be very different?
Yes, because the output impedance of the transmitter does not in any way affect the SWR. The proviso here is that your output power must be within the range in which the meter is accurate. Some meters do poorly when the output power is very low.
4) As long as the PA does not self oscillate, is it always a good idea to tune the output of a transistor PA (of unknown output impedance) to read the maximum power of the power meter set between the tuner and a 50 ohm fully matched transmission line and antenna?
Generally you adjust the tuner with reduced power. Once the tuner is adjusted, then raise the output power to the maximum if your goal is to measure its maximum output power under the condition. Keep in mind that this often needs to be a carrier measurement as most meters (even many so called peak reading meters) aren't very accurate for voice SSB.
5) Is it a good or bad idea to tune the input of a transistor PA (with unknown input impedance) in order to get more output (still well within the power limits of the PA, say getting 50 watts from a 100 watt amplifier, but driving it with less power with a tuner between the TX and the input of the PA)?
You need to tune the output circuit of a tubed transmitter first in order to avoid damaging the tube. The best way to do this is tune it into a dummy load. Once you know where the settings are for a sub-band into the dummy load, you can write those down so that you can more quickly tune your output circuit in the future. Once you have the output circuit tuned, you can switch to the tuner, reduce power and then adjust the tuner or trigger the autotune procedure. Once the tuning is done, raise your output power as needed.
The adjustment of the output circuit of a tubed transmitter also ensures that the transmitter is not putting out harmonics. Failing to tune may cause the transmitter to output harmonic energy which can result in strange SWR and directional power readings. So besides tuning to protect the tube, tuning also ensures only the desired frequency is output from the transmitter.
- Glenn W9IQ