I have also found that the HEIC flew the Red Ensign in the Atlantic if they were North of St. Helena.
Also here are some of the Merchant flags of Portugal
http://www.crwflags.com/fotw/flags/pt~hist.html
and Denmark.
Attachment 17815
The modern national (so also the merchant) flag was defined in 1748. Before that this was the usual form of the flag, apparently, with the cross centered. That such flags were actually used confirms this historic event explained here regarding the defacing of the naval flags for use in the Mediterranean:"Regulations dated 25 March 1757 inserted a white panel with the Royal cypher to the intersection of the cross in the Danish flag for ships sailing in the Mediterranean. This was made necessary because of increasing Danish trade and the conclusion of treaties with the North African states who on payment of tribute undertook to respect the flag of Denmark as long as it was distinguished from the flag of Malta. This variant civil ensign survived, with changing cyphers, until it was abolished in 1867.
Rob.