If you are looking for CMYK output why are you setting the colors to spot? Just set the Illustrator color to process and make a 52|100|0|25 process swatch in InDesign.
I make big format prints for customers. So I get many PDF files from my customers. Each customer gets his files from all over the world; I cannot explain the hole world how to deliver PDF files.
I try to do as less as possible to correct PDF files. So how can I setup Indesign, so spotcolors from imported PDF files are untouched?
TXS! grz Paul
In CS6 and later the Pantone+ spot libraries are defined as Lab, so when you place a file with a legacy Pantone spot CMYK definition the newer library is used.
In a composite workflow spot colors have to get converted to process somewhere, so you could set spots to process in Illustrator, maybe via scripting, which would keep legacy defined CMYK values.