Did both Crocodile and Smoker use the artificial rain powder in Alabasta? By reading the manga and rewatching the anime I reached to this conclusion - 
Rain didn't fall in Alabasta for 3 years, but before that it did only in the capital and not in the neighbouring regions. 
When the artificial rain powder is used, the location where it is used gets more than average rain and nearby areas don't get any. 
Since by good faith we know the king wasn't using the powder or had any knowledge of it being used, could it be that Crocodile was using it in the capital from some hidden location which resulted in such a phenomenon and after he stopped using it, say the 3 years that no rain happened was the time natural weather was reconstructing itself and whether or not Crocodile was defeated, it would have rained nonetheless??

And secondly if Smoker had used artificial rain machine from a ship after the fight (couldn't figure out whether it was the case or not as he says when asked, he will never break the law but it is shown such a ship is there in the back) , how was he able to make rain the whole island??
No, only Crocodile used the rain powder. Smoker was specifically asked by Hina if he used the dance powder and he said no (chapter 212). I know you stated this but it's firm proof until it's said otherwise.