I've seen champions use same hand chalking and other champs doing the exact opposite. Just a personal preference, I'd say.
For me, the main objective is to effectively chalk the tip without 'raining' chalk dust down onto the shaft or my other hand (and for goodness sake, not on the table).
I consider effective chalking to be a swiping motion as opposed to drilling and doing so while the cue is at an angle so as to avoid the aforementioned dust storm.
For me, using my stroke hand to chalk (swipe) feels more natural. I'm sure though, either hand could do the job just fine.
However, I may have to rethink all of this after reading in another thread that how you chalk your cue may have some correlation to your sexual orientation.
Best,
Brian kc