If you will deliver print-ready-pdf then do it in X1. X1 doesn't allow RGB-colors.
Since quite 10 years was introduced PDF X4. This is a version that save transparencies native and is compatible to the AI-format. X4 allows RGB and CMYK colors.
But attention with fills and transparencies (shadows are transparencies too) they will be in all 4 print colors so a manual recoloring in AI is necessary if they must overprint or be only black (K).