A number of people have used the idea that SHADO was dealing with more than one 'racial' or 'political' group on the alien planet.
And there are other explanations - In QoP, the alien seems to be trying to communicate with SHADO, then 'gives up and goes out to die' when the other craft shows up.
But what if the motive for the alien using SHADO's frequency was to lure one or more senior officers out there to be killed? Attacking the mobiles would simply alert SHADO that it had been a trap whose bait hadn't been as effective as needed. The alien was killed to keep him from falling into SHADO's hands and to give weight to the idea that there were 'friendly' factions. Something they might be able to use in the future.
And in ESP - Croxley appears to be channeling an alien who doesn't understand why they're under attack - but the aliens
deliberately targeted Croxley's house to kill his wife. And they don't understand why humans are so against them?
As to the aging issue - while the first captured alien may have been a 'real' alien and reverted to his true age when exposed to Earth's atmosphere, but what if the other 'aliens' were captured humans - brain-wiped cannon fodder - and so were not only younger, but 'immune' to Earth's toxins.
Hey, I write Perl - if there's only one solution, you're not trying hard enough.