System Information
Operating system: Windows 10
Graphics card: GeForce RTX 2080 Ti

Blender Version
Broken: 2.91
Worked: None

Short description of error

When I have an object that has boolean modifiers on it, for example some other objects used as cut-outs for the object, the object and all of these hidden objects all get exported together. I've ensured all these auxiliary objects are marked as hidden and un-rendered, and they don't show up when I render. I've also ensured that all the modifiers are marked as rendered as well, and when I export I check the "Apply Modifiers" checkbox, but this appears to have no effect. What I've had to do, in order to preserve the modifiers and be able to change them later, is to duplicate the file and apply all the modifiers in the duplicated file, then export, but this step shouldn't be necessary if the "Apply Modifiers" checkbox works as advertised.

Exact steps for others to reproduce the error

1. Create a mesh object; let's call that Foo.
2. Create an intersecting mesh object, Bar.
3. Add a boolean difference modifier to Foo, with Bar as the target. At this point, Foo and Bar are both visible.
4. Make Bar hidden and also uncheck its render setting so that it does not get rendered. Now, only Foo should be visible with a Bar-shaped chunk taken out of it.
5. Export an STL of the entire file or just Foo.
6. STL includes both Foo and Bar meshes when it should be identical to the Foo-minus-Bar shape in (4).