"1884 The first known ‘City shirt’ is created – in black, with a Maltese-style cross. Some say this is because of the club’s strong links with Freemasonry in the 1880s, others believe the white cross proves the link with St Mark’s was still strong"
From the OS history.
So basically no-one has a bloody clue.
St Marks was of course a Church of England place
http://www.genuki.org.uk/big/eng/LAN/Go ... Mark.shtml
So why an obviously catholic symbol would link to this who knows? 'Maltese-style' means nothing as I said above because that just means it is derived from the crusader orders. Freemasons is therefore obviously a possibility, and they do use Templar symbols like this:


Most likely some bloke liked the look of that symbol - must be difficult to think of a badge from scratch in a hurry - , or got a job lot of those badges from a local trader left over.