How to choose romanization for non-Latin script in an otherwise Latin script text?
For things that you won't publish, you can adhere to a standard you choose, for example writing in the Korean script using LaTeX.

It's difficult to talk more specifically than that because journals have their own requirements, which can have more to do with their typesetting systems than academic rigor. 

If a journal publishes your work with ambiguous transliteration, you may be able to keep an alternate copy on ArXiV. (N.B. I'm not sure it's kosher to do this but I suspect it's fine as long as the alternate version is designated carefully.)