If flattening is needed on an RGB object, it will be put in CMYK (+ spot colors) by the flattening mechanism. Objects created by the flattener will always be in CMYK + spots color space.
When the Resolve transparency checkbox is not selected, overprint problems will not be flattened, unless the Resolve overprint checkbox is selected. This means that other transparencies (at least those not interfering with overprint objects) remain in the PDF.