Yeah unfortunately a lot of mechanics do sometimes think it is OK to clamp anywhere but the seatpost and the ones who at least know they really shouldn't will always say "well it is fine just for this" or something of that nature. It was a poor decision on that mechanics part but I do know on bikes they don't work on often that are like that it can be hard to know really a good place to clamp that won't cause imbalance and while they should never have done it is good they are owning up to it and actually reached out to everyone to get it fixed and make sure it is good to ride. I would say if they didn't own up to it and try to make it right there would be a solid complaint but they were human and they made a mistake, realized the mistake and sounds like they are doing right by you. Sure they shouldn't have done it in the first place but we have all done things we shouldn't have done it is part of life. It is not to say it is right or wrong it just is what it is. If they keep doing it then there is a problem.
Mechanics can sometimes get cocky I know a lot of them that just say "I got this" and they really don't or they try and rush for a customer maybe they both speak the same language that isn't English in a typically English speaking shop or they have some sort of interest in the person or bike and just ram through it and make mistakes. Every good mechanic should take their time and do it correctly and if they don't know how to do something they should always ask questions no matter what the question. One cannot know everything (except maybe
Sheldon Brown but I am sure even he had to ask a question once and a while) and those who understand that can be really great mechanics or just great at life in general. You have to be thirsty for knowledge and be willing to learn new things and old things and know when to do something and when to stop and say let me ask a co-worker or call another shop or call the manufacturer.
Co-Motion makes great stuff I have a single Cascadia from them and it is fantastic but I would one day love a tandem and someone who would willingly ride on the bike with me...LOL
I would trust them if they say the bike is safe to ride but I would certainly make sure to get it in the shop when you can and maybe see if you can schedule something so you can leave it for less time. It would be an excellent chance to get the whole thing overhauled anyway and fully refreshed. Good luck with everything!