The stone towers are something of a trap, especially since you don't get the ability to repair them until the next biome. If you want a troll shelter in the black forest, look for those above ground crypts with the sheltered entrances. They are indestructible, and at worst you can go inside. But remember that log trolls do area damage, like your stagbreaker.

Usually I do dig a trench around my base, lead them back there and shoot them. If I want to hunt trolls and don't have a base nearby I'll dig around a 3x3 floor (or 6x6m) minimum area and do the same thing. Anything smaller than that and you'll be in range of the log. Rocks you have to dodge but they're easy to predict.