Using Quark r1.5-127 and ARL 1.3-20 on Forge 14.23.4.2756

Chest in a boat will disappear after some time of riding in the Boat causing the inventory to become inaccessible and instead showing the vanilla boat interface when opened, breaking the boat will drop the chest as well as any items that were initially stored within it.

If you exit and enter the world the chest inventory is restored.

Is this still present?

Yes, still present in AutoRegLib-1.3-28 and Quark-r1.5-150