I don't think that you got hosed in any way... and I know most shops will toss out that little nut on the presta valve, and many more will toss the plastic cap. It's just one more little piece that at some point in time is going to end up as litter. If you want these, by all means say so when you bring the bike in, but if you don't specify that, I wouldn't be surprised.

I guess I think you were treated fairly in terms of what they did, but they failed when it came to their attitude. It requires zero effort to be polite and really only good can come of that. For example, when you dropped the bike off, instead of a flat no, a simple "I'd love to help you out, but I've promised persons X, Y and Z these jobs by the end of the day and I just don't have time" is a little more polite. This is where I think things went wrong. Obviously the person who called you could deduce that since you were out of town, you couldn't come get the bike. At that point, whether they are glad the bike is still there or not, they should say "Oh of course you can get it tomorrow, we just wanted to remind you in case you forgot, people forget all the time". End of story, no big deal.

Then when you pick the bike up, the mechanic should have been more understanding, but sometimes mechanics don't get people-skills training, so I would never be too surprised to get a gruff mechanic (remember, he is probably getting it from his boss when the work starts piling up). And to change your new tube on the spot was pretty nice of them, so I think overall their heart is in the right place, they just didn't really express it properly. It could get better as they get to know you, but maybe they just aren't all that much of "people" people. I wouldn't hesitate to go back, but I would understand why you may not want to. But at the same time, if I was the manager of the store I would have a conversation with my people about how to handle the situation better.

It may be worth your time to write to them about your concerns and see what they have to say. If they respond positively, then they care about your business and it may have been an off day/week where they were slammed. If they blow you off, maybe they don't care and it isn't worth your time. Hard to tell for sure from the story above though.