Official Timing seems same!!
Karjat & Lonavala are Technical Stoppage too & hence cant be skipped (I guess it halt @ Khandala too).
When train is been started & is SPL/Experimental, then stoppage are been granted to check feasibility &/or garner revenue!!
Past Summer rush, other stoppages wouldnt have been feasible (revnue-wise) & hence are discounted!!