"Write BOM" checkbox in config panel, influences the writing of UTF-16 files, too. IMO it must influence only UTF-8 files, as they, really, may be written with or without BOM (without is the standard) - but UTF-16 files must be always with BOM, otherwise they will incorrect files (not readable). I think, this is a bug; at least I'd like it more this way. Or, as a compromise, may be taken a "Write BOM" checkbox at export window too, not only in config.
I've just revisited this topic and consulted the Unicode Standard (Version 11.0). According to 3.10 Unicode Encoding Schemes, it's possible to also write UTF-16 without BOM.