BoltDB author here. Yes, it is a bad design. The project was never intended to go to production but rather it was a port of LMDB so I could understand the internals. I simplified the freelist handling since it was a toy project. At Shopify, we had some serious issues at the time (~2014) with either LMDB or the Go driver that we couldn't resolve after several months so we swapped out for Bolt. And alas, my poor design stuck around.
https://news.ycombinator.com/item?id=30015913
Теперь вспоминаем, что Bolt и в etcd тоже живёт. Ой-ой...