AFAIK, the spots in placed PDFs (or EPSs) are NOT remapped during "normal" PDF export - they would be left alone. So if you had CMYK-based alternates in the original and then exported, you would still have CMYK-based alternates. Also, if you have different spots of the same name, they will also be left alone.
HOWEVER, if you are exporting to PDF/X (any flavor), THEN we will remap (and consolidate) the Spots due to the PDF/X rules.
Thanks Leonard, I will test and post back, I am no longer in day to day production so my memory can sometimes lead me astray!
EDIT - Of course, things were deeper than I remembered them!
Test 1: Photoshop DCS2 file with RGB alternate colour, placed into an ID file with no spots in the colour palette, exported as Press Quality PDF = Alternate Colour is now CMYK, so there was a conversion for an RGB spot colour definition. The colour imported into ID with a default of a CMYK colour build definition and exported with the same.
Test 2: Photoshop DCS2 file with L*a*b* alternate colour, placed into an ID file with no spots in the colour palette, exported as Press Quality PDF = Alternate Colour is now CMYK, so there was a conversion for an L*a*b* spot colour definition. The colour imported into ID with a default of a CMYK colour build definition and exported with the same.
Test 3: Illustrator Native file with L*a*b* alternate colour, placed into an ID file with no spots in the colour palette, exported as Press Quality PDF = Alternate Colour is now CMYK, so there was a conversion for an RGB spot colour definition. The colour imported into ID was L*a*b* colour build and exported with CMYK build.
Test 4: As above in Test 3, however the PDF export was set to no colour conversion. The resulting PDF colour build was exported with L*a*b* alternate spot colour build values.
Test 5: llustrator Native file with L*a*b* alternate colour, placed into an ID file with an existing RGB alternate build spot colour of the same name. PDF export was set to no colour conversion. The L*a*b* alternate colour build in the PDF is now RGB, not L*a*b* - even though the export was set to no conversion, the pre-existing spot colour alternate build changed the alternate colour build.
Test 6: Photoshop DCS2 file with RGB alternate colour, placed into an ID file with an existing L*a*b* alternate build spot colour of the same name. exported as Press Quality PDF set to no colour conversion = Alternate Colour is now L*a*b*, so there was a conversion for an RGB spot colour definition. So the DCS colour was ignored and the ID colour was used instead.
Conclusion: things are a lot messier than I remembered them to be!
If one uses consistent file formats, consistent spot colour names, consistent spot colour builds, pre-populates ID with the desired colour name and build and also exports with the desired setting (convert or no colour conversion)...then the results will become predictable with a little bit of experience and experimentation, which is how I remembered them to be when I was building my own files.
Stephen Marsh