The bass neck ended up on the bottom of my Dano due to the 12-string bridge being on the top; it started as a 12/6 but I replaced the 6-neck with a baritone which I strung as a bass6.
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When Danelectro released their guitar/baritone, which is really a guitar/bass6, they put the longer neck on the top. For me playing the bass neck can be a bit of a stretch but at that point I simply reposition the guitar against my body for better playing. I do like having the 12-string neck closer as it allows for more accurate playing so I would opt to leave it as is if given the choice.
So it really depends on how you play. If you play with a low-slung 6-string, then putting the bass on top may work better. Regardless I find I adapt to what I have as there's yin and yang in everything.