I have carried 2 spare batteries on long trips on rail trails like the Katy Trail, the GAP in PA, and the C&O Towpath which can be fairly rough. You're right, the battery length can make it a little awkward. I got some large bubble wrap at work and made a couple of sleeves and inserted my batteries in them--protects them and keeps them warmer on cold days. I have a great Racktime rear rack and hang an Ortlieb Back Roller off each side, 1 battery per bag. I take it a little easy on bumps to keep the battery from bumping around, but it works fine. On long trips I just stuff soft things like my little tent, sleep bag, clothing around the batteries in the Ortliebs for added protection. Never have had issues and have ridden many hundreds of miles this way.