Hi,
Yes, VM Template - Puremart has this drawback, and this issue occurs when the "custom field - generic child product" option is applied. Because the "add to cart" button we have used in this VM Template is very sophisticated and it includes some extra <span> </span> TAGS.
Another drawback is; IF you are using generic child product, the parent product must be "not-orderable" because, (you are right), the product will be marked as "out of stock" even though there are some stock left in child products. This fact is also addressed in our DEMO:
www.flexiblewebdesign.com/virtuemart-2-template-puremart/index.php/test-category
if you look at this product:
www.flexiblewebdesign.com/virtuemart-2-template-puremart/index.php/test-category/diesel-sweater-generic-child-variant-detail
It says: .....But this custom field option is not a convenient way for stocking. Because if the BLACK is out of stock, this product will be marked as "out of stock" in category browse page even though there are some stocks left in other colors.
So why don't you use "custom field, VM Stockable variants" ? it is a better way if you have stock-able variants.
regards.