I think "no biggie" is a rather large assumption. Imagine if it were the other way around. We send a mother ship off to some alien world where our shuttle accidentally lands on some alien life form. But not to worry because we just happen to know how to fix these aliens and keep a ready supply of whatever they use as nourishment ( assuming they even eat in the first place ) back on the mother ship, where we can hang around for a few days undetected, and then deliver the alien back to its native environment, also without being noticed. We can do all that, but can't notice them approaching us in the first place with a lit up primitive ground vehicle that stops to let one of the aliens out so that it can run up and get caught in our landing gear? Sure, why would we have any problem believing that?
I can "easily go for the fact that possibly" it was all a hoax before I would "easily go for the fact that possibly" aliens did their version of road kill on Travis Walton, but fixed him all up and dropped him off back at the local gas station.
I think it's done in a hospital while under life support by doctors who are experienced and equipped and knowledgeable about treating humans. I think it's a big leap to assume that aliens are that well prepared to deal with the medical needs of a species alien to them. I'm not saying it's impossible. Just that I don't think it's something that should simply be taken for granted.
That would mean that when they were building their spacecraft ( as you suggest ), they took into account that they might need to perform medical procedures on whatever alien life forms they might encounter at the destination, engineer that capacity into their spacecraft, and be prepared with a sufficient working knowledge of alien physiology and biology to treat them and leave no evidence of treatment behind that the alien's own doctors could detect. As a consequence pulling this off would require a whole bunch more fantastical assumptions, like that they can almost instantly assess something as complex as a humanoid alien life form and produce the medicine and tools needed, or that they have advance knowledge, which implies round trips of previous expeditions and spacecraft upgrades to accommodate medical bays for humans.
Apparently the aliens just happened to have an oxygen mask handy on the mother ship, which implies a ready supply of masks molded to fit the human face and a knowledge of what we can breathe. Sure, it's all possible, but to say that having all these requirements instantly met are "of the smallest of consequences" is trivializing just how much would actually be involved and required. Yet these same ultra amazing super sophisticated aliens who kept their mother ship and shuttles undetected for at least several days while they fixed Walton up were still so inept as to let a pickup truck full of forestry workers spot them, stop, watch them, and even allow one of the passengers to approach them and get zapped?
OK Goggs, I'm a believer in alien visitation. So I'll grant that maybe it all this happened just like Walton said it did. But I'm not going to overlook these other factors. I remain very skeptical of the Apache-Sitgreaves National forest incident a.k.a. the Walton incident, and I think that it's the most reasonable point of view.