I always understood "bis" is the Indonesian word, and "bas" is the Malay word - I remember the KL perhentian bas besar, near Jl Petaling.
Using the English spelling "bus" would read aloud like "boos" - incorrect and confusing. A Dutch speaker would read "bus" with their particular "u" sound, which would sound to me like "bis". So I guess there's some Dutch influence in Indonesian loanwords?
I don't know any of the EYD rules to refer to, so this is all just a guess. -.-