It is a progression item so it gets a boss.

Maybe a stone shovel so you can dig in dirt?

Flint vs Stone --- you don't always spawn in near a shore for flint. Stone you can pick up anywhere. And if you die and get stranded someplace it will probably be easier to make a stone ax than a flint one.

Upgrades for crafting station ... you need to upgrade the crafting bench to make flint and deer skin stuff. So it teaches you the basics of upgrade items.

side note - I also think this is why you can get leather scraps everywhere... if you get stranded you can at least make a raft.