In Linux, the dot (period, full stop) is just another character. It has no special significance except for tools like grep (which allows it as a substitute for any other character). Unlike MS-Windows, Linux doesn't take special notice of periods in a file name unless they are at the beginning (which makes the filename "hidden").
It is true that some filesystems -- like the ISO filesystem used on data CDs -- will omit trailing dots from filenames. But the hard-disk filesystems shouldn't force that. Maybe it's the B2 software rather than the operating system?
OTOH, I've found that some CDDB entries omit trailing dots; the Kingston Trio song "M.T.A." often shows up without the trailing dot, if it has any at all...