Just lay rod horizontal when pedaling.
Either I don't know what you mean, or you aren't thinking that one through. You can't lay your rod horizontally in front of you and pedal. It will get in the way of your pedalling. That's one of the most aggravating parts of having a pedal boat for me, I can't just lay my rods down in my Outback. I HAVE to put them in a rod holder somewhere.
Now, you can throw them in the rod holders behind you just fine, but it will involve more turning around, which might get old.
I'd say just don't install them yet, see how you like it, and if you find yourself never missing them then don't install any. Taking other people's preferences won't help much, as everyone is different.