I see that objects are positioned in the STL "as designed", that OpenSCAD does not helpfully center the model, or base it at Z=0, or anything like that.  That's an essential behavior for your plan. It's also an essential behavior for multi-color / multi-material models, at least until we emit those into formats that can directly handle them. We should probably document it somewhere (including in comments in the STL export implementation) so that nobody helpfully "improves" it.