The first big question is what your inventory multiplier is set at.

If it's at 1x, then everything in your ships cargo containers will exert full effective mass effect on the ship. (gravity, inertia, etc)

If it's at 10x, then the effective mass effect of items in the inventory is only 1/10 (but the full mass will still be shown on the HUD).

The mass mitigation thing is done so that ship designs will fly the same at the same % cargo loading whether you're playing 1x, 3x, or 10x inventory.

So, for example, the little atmospheric miner I use right now has about 140 tons ship mass and can carry an additional 200 tons.

When I play normally (I play at 1x inv), I can load it up to about 340 tons before I need to unload things.

If I take it over to a 10x world, though, that 200 tons becomes 2k tons -- the mass indicator will read ~2,140,000 kg before I need to unload it, even though it can only fly up to 340,000 kg at 1x inv.

So, I'd suggest switching to 1x inv and trying your experiments again.