To be clear, Rin and Len are voiced by the same person, yes, but they don't use the same recordings. The voice actor recorded twice using two different voice tones. So you could do it this way. Doing it this way would be more likely to make the two characters sound truly different from each other, but you'd have to be able to change your voice enough to make it sound like different characters. Unless you just want two characters with similar voices which is also an option.
Otherwise, like already stated, you could use flags to change the voice tone. No matter what you do its going to sound in some capacity similar to the original recording, in particular the pronunciation will always stay largely the same, but its not unheard of for a particular flag configuration of a VB to be used for a separate character (or a genderbend)