I'll give my 2 cents as a female working in the construction (albeit not residential) industry. I'm a plain speaker, so please don't mistake my verbiage for scolding, rather it's just a unemotional opinion as I see the situation as you have told it.
Respectfully, your use of "we" is possibly a small part of the issue. There should be no "we". Your daughter and her husband are grown adults who own a house and got their roof fixed. They should handle it. No one is going to respect a fully grown married couple having Mommy & Daddy go to bat for them. And no young couple will learn how to manage their own lives if someone else does it for them. Yes, parents can be a storehouse of invaluable knowledge and experiences, but all this "we" stuff is not necessary. Honestly...consider that the fact that they called for 12 days leaving many messages is likely a small part of the issue. One or two messages should be sufficient. THEY HAVE HIS $$$, if he wants it he will return their call. They have him by the short & curlies here and no amount of complaining will get the Owner to call them back to come to a face to face meeting and genuinely apologize. Him or Her wanting their money will. They might think he did, but in fact what he did was tell them (or worse, you & your husband if you are there ) what you want to hear, get his check and leave. If she can't open the door for the FEDEX guy cause some used her bathroom w/o closing the door and or because they swiped some of her apples and she didn't call them on it there and then, well I'd say her issue isn't really someone using her bathroom w/o closing the door or someone swiping her apples. Look - I'm a Mother and my young adult son just bought his first home. Did we help, did we offer our opinion, yes we did. We hand held when asked, but we also stepped back and let go of their hands so they could do it themselves - let them go thru the process and learn, including having contractors come out to do a few things.
Yeah, that's a new one to me. We have folks come onto our farm for a few days each year to do some crop specific work and we always get a port a potty for them.
Most of us would, but OP's daughter should consider the cold fact that the owner of the Company may not have any employees, he could very well sub out each job. You never know. Obviously it's not always the case, but it is always possible. Plus - many of our employees have vehicles with different state tags on them. It's not my job to police what state they have their vehicle tagged in, and I don't think to much about it. It's not a entirely out of the norm situation.
She's going to have to let it go. It's minor in the grand scheme of life, and probably minor in the grand scheme of major home improvements. Going forward, if she didn't do so when having her roof replaced she should have asked for a current copy of the Contractors Insurance indicating work comp in her state, and gone out to see if the roofers were tied off. She should have asked the guys who they worked for/proof they worked for the roofer if she wondered who they were. If she was uncomfortable she could have told them to stop and called the roofer right then and there.
This is a excellent opportunity for your daughter to learn how to express herself and her needs to someone she contracted with and paid to do work for her, and a good lesson in what to do in the future prior to getting to this point in a situation.