No issues at all for having two applications in process. Having NDVO as your VO will give you a safety net....in case you have to leave Canada for any reason (God forbid), then you can be in India for PP stamping. But if you have Buffalo as VO then you have send your PP to Buffalo for stamping which may not be a possibility.
Be aware that when you are asked for stamping ....you will have to make arrangements for your PP to be mailed to NDVO and received at an Indian address. VO will not mail your PP to Canada.
GOOD LUCK...
Mitali