It would be unusual to me to see million or billion used in academic scientific contexts, except for a few cases where there would be absolutely no ambiguity (number of people on earth or age of rocks, for example, would only fall under the American/modern usage of billion), and even in those contexts, only for loose descriptions (versus reporting of data). (I did a brief Google Scholar search for both million and billion; although there were many many results, most seemed to be referencing either authors surnamed Million or Billion, or the use of the terms in these loose forms or in the context of geology, as in "three billion year-old rocks)
I can't think of a circumstance where scientific notation or use of SI prefixes would be a problem when writing for an scientific academic audience. If writing for a lay audience or outside the hard sciences, it might make more sense to use million/billion: most respectable outlets will either have a style guide or refer to another established style guide for proper procedure. It seems like the BBC and University of Cambridge embrace the 10^9 billion and do not caution specifically against its use, only noting the previous definition. Certainly in no context should you use billion to mean 10^12.