I think you are over-thinking this a bit...
There's a tick-box on a customer entry screen.
It either gets ticked, or not, apparently depending on some interaction with the customer.
I can't accept that ticking a box determines the "mood" of the discussions, and that someone has to, somehow, be annoyed now because there is a box ticked on a screen.
I did notice that you did not say that you were poorly treated at your last visit, only that you saw a checkbox, and now your confidence in the store seems affected, and for no good reason that I can see.
In the end, it is probably not the shop's responsibility to educate a customer about consumer law. The shop only has to comply with the law, and it's on YOU to have some awareness that you might have an issue that would fall under that law's protection.
And, filled up with knowledge, you ask. And, assuming that you are accurate about what you saw, the shop would tick that box, as a result of a discussion with you. I don't think you can read anything more into it, than that... It would be similar to the other form entries that normally happen with a service request.
So, it would appear that the repair shop wants to keep track of the fact that you asked about that, and that may be a requirement on their end. Maybe that's the reason. Not a bad reason, IMHO.