How come 'à' is used to mean 'with' in the sentence 'surmontées par une grande église romane à clocher carré'

You can't simply translate French prepositions to English in a 1-to-1 fashion. The use of à in this sentence is similar to these examples:

une glace à la vanille -- ice cream made with vanilla (vanilla ice cream)
une soup aux broccolis -- a soup made with broccoli (broccoli soup)

still don't understand as its not "made with a square clock tower"? and it's also not a food? (to which I understand the use of 'à' with foods)...I just don't get how to know when to use "à" as opposed to simply "avec" with these examples?

I notice that in French the James Bond story The Man with the Golden Gun is 'L'homme au pistolet d'or'. It's the same difference - English people tend to think in terms of 'with' while French people think more in terms of 'for / to'. It's just a different way of conceptualising this kind of associative relationship.