Hi Ben, the .stl format does not have any method for containing multiple objects, it's only really intended to contain a single object and it only has a place in the file for storing a single object name. So the "merge object with the same name" doesn't have any effect on STL exports.
You can probably get away with putting multiple objects in one single stl file if they don't touch each other, but when they are touching it's difficult for the program that is receiving the file to be able to tell them apart.
You may have to export each object to its own separate .stl file, or possibly use a different format like obj format which does support having multiple labeled objects in a single file.
It's hard to say for sure what you should do because it's dependent on the particular slicing software and capabilities of your printer.
- Michael
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