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If the first pass pseudo BD structure fits on a BD25, there is no need to do the backup. That avoids a re-encoding of the files, which adds errors to the encoding. The fewer the encodings the better.
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This assumes that the imported MKV files are Blu-Ray compliant. In my experience the vast majority of MKV files are not, and trying to keep them intact will lead to a lot of wasted time and frustration. I would recommend you plan to ALWAYS reencode unless you have created the MKV files yourself from original blu-ray (or DVD), and they have not been reencoded anywhere in the process.
[Edit] Just a side note -- there are also DVD formats that are not BD compliant, but they are rare enough (almost nonexistent) that you can pretty much ignore that worry.