It's very possible that the staff member felt scared of the ramifications of not doing this. I can just see some horrible TRA going on a Twitter rant, with pictures and videos, naming and shaming the shop and the assistant. Remember, these people are prepared to ruin anyone for their righteous cause.
Jumped up, snotty upstarts with a bit of sinister power, going into shops and demanding that they fly particular flags is reminiscent of every totalitarian regime going. Transactivists might as well end every sentence they utter with the words, 'Or else!'