Blu-ray format already uses MKV as the default file format. Most encoders suggest to use MKV format and codec because it can store high quality streams in medium-high file sizes. Nowadays, you can use most of the known converters to convert the MKV to other Blu-ray format, but it has no meaning in doing it. MKV stands the only viable solution to keep it.
Of course, to directly create a Blu-ray disc, use Nero or any other compatible burning solution and burn the video file as Blu-ray disc. The software will take care of the encoding methods and chapter creation.
Yes, you can convert the MKV file to another format using an application from this category. For example, WinX HD Video Converter Deluxe is an application that may come in need for this type of operation.