Canning Tomatoes: When are they too blemished and why does it matter?
It's exactly what you suspect: blemishes indicate the possibility of contaminants, or provide an avenue for invasion, inside the tomato flesh. And while pressure canning kills a lot of organisms that would cause contamination, the higher the bacterial/fungal load, the more likely a few spores or cysts are to survive(PDF, large) and eventually germinate in the canned food.
To quote Michigan State University:

... the tissue damage and a rise in pH can create conditions that promote the growth of other potentially dangerous microorganisms ... The condition of the food item will not improve once it has been canned or frozen.

Tomatoes are particularly risky because they hover around the border of being acidic enough for low-pressure canning, and most home processors don't want to kettle them too long for texture reasons.
So it may be &quot;granny wisdom&quot; but it's solid, scientific granny wisdom.
In terms of your specific blemishes: yes, the skin splitting on otherwise fine tomatoes is still a problem.  One thing that does is provide an avenue for botulism spores to embed themselves in the flesh of the tomato.  Normally when you can tomatoes you remove the skin, and with it the vast majority of spores.  But any spores that got into that split are still there.
(note: the long PDF on heat-treatment was included to show that spores die over heat/time as a percentage of the spores originally present.  Hence, more spores, more risk)