So is it worth pursuing the idea that the 2 families are connected? Its either pure coincidence they have the same surname or as its been pointed out, the baptisms have been organised together and the curate informed.
It's almost impossible to answer that, but there are a few factors that you might want to consider:
How common was the surname Ellis in that parish? If it was unusual, that probably increases the chances that they were related.
Were there any unusual forenames that crop up in both families?
Did they live close to each other or follow similar occupations? (Not always easy to establish if it's not mentioned in the register, but consider things like tithe maps, land deeds and manorial records.)
Did either of them leave a will mentioning members of the wider family? Or are there any wills from earlier generations that might mention them both?
Sometimes all you can do is trace both lines backwards as far as you can to see if there's any point at which they join, but it's also possible that any connection could be before the start of written records. Good luck!