OK, then I get the problem you have spot colours AND you don't want live transparency. Some RIPs can handle this but not all. Some systems you will get very strange effects if you wan't to remap a spot colour that interacts with transparent effecect to a CMYK object. The reason this is problematic is that to maintain transparency the spot colour normally has an aphachannel masking it, and an apha channel to where it is to be knocked out. Converting the spot colour after flattening will destroy the link that says these two masks will match up and overprint.
What it means is that transparency in Spot+CMYK will not work unless overprint is handled very carefuly, converting the spot to CMYK downstream will only work on certain RIPs that have looked at this workflow as a whole (AGFA have a special routine to map colours keeping overprint, I think others have similar solutions, but can't say for sure).
The other alternative is to go PDFx4, but that again requires a good colour management module in the RIP, and if you are planing on using relative colometric, you will want a RIP that has possibility to have BPC (IMHO).
This is ofcurse how I understand the problem, and you may find others that can complete the picture.