I would also like to know if there's a better way to do this.
Right now, I think this behavior is expected. Blockbench seems to only be able to generate textures that are rectangular in nature.
However, for low poly models, your faces are not necessarily flat. I've noticed when trying to manually create a sphere, that some faces will end up with a slight amount of curvature. Also, unlike minecraft modeling, your faces are not enforced to be rectangles, but can be trapezoids and other four-corner shapes. From what I can gather, those "odd shapes" are actually the true shape present on the model face and it is actually more unnatural for the UV to stretch to fit a rectangle
Someone please correct me if anything I said is wrong! I still have a lot to learn 🙂
I'm super curious to know if there's a better way to handle low poly texture generating, I'm also having a lot of trouble syncing up pixel perfect textures on my low poly models - maybe it is not possible without a lot of manual labor