It seems part of the ship design tonnage bug was fixed, but there is still another tonnage bug remaining. When you click "Update Armor" (even with no new armor tech to upgrade to), it erroneously changes the armor amount and ship tonnage. When you select a different ship design and then click back, the armor values are reset to their "true values".
Also, when you add components to a ship and remove them, the ship again miscalculates its tonnage. Fixed again by selecting some other ship design, and then going back to the one you were working on.
Example: My test ship with 10 armor layers is 2,312 tons. I add 1x "cargo hold standard". Ship is now 37,950 tons. I then remove the "cargo hold standard". Ship is now shown as 2,339 tons, somehow.
Definite bug, easily reproducible. It was like this in 1. 0, as well. Seems related to armor calculations.