Not everytime, just occasionally. Is it harmful? How can I correct it?
Understand what the noise is.....
The noise occurs because of flux leakage. When a transformer winding is delivering current, it generates a counter magneto motive force that opposes primary flux levels. This causes the impedance to drop and the primary draws more current to restore flux levels, but it also tends to push flux out of the core into the air. The flux pushed out into the air around the transformer can move other things, like steel covers.
This flux leakage occurs over a few cycles, not just one. Starting at zero does not fix it, it generally makes it worse. Starting on the declining edge of the top of the waveform is actually best, but still not a reliable fix because it generally involves a few cycles anyway.
The cure is to let the load slowly die off. This can be done by starting the primary through a resistance of a few ohms, perhaps a dozen ohms. The time delay can be extremely simple with only two components, a relay and a resistor.
You could get a 12 volt dc relay and connect it across the supply output, and have that relay short a 10-20 ohm 10 watt resistor in the primary, or you could get a 120 volt AC relay and have that relay coil across the transformer primary. Again it would short the series resistance in the mains but between the mains and the relay coil and primary.
The advantage of this system is it is "self-timing" and removes the resistor when the supply is nearly at full voltage (depending on the relay, at about 70% of full voltage). It requires no capacitors at all, and will work flawlessly. With a 12 volt supply you could copy what is done in the ALS1300 and even use the same parts, which is a 12V dc relay and resistor.
The thunk is probably not harmful, generally the only component being taxed is the off-on switch. In the Ameritron series of amplifiers I added step starts only to increase switch contact life and to reduce the PERCEPTION of a problem by customers. Measurements showed nothing else was unduly stressed by the inrush, not even filaments, but it did greatly improve contact life in the primary switching and got rid of acoustic noise.
Unless your Astron eats up power switches, I would probably leave it alone.