Do these other pages have access to the WP functions (you say the sit within the template)? If so then it won't be a problem and if not, you will just need to create sql commands to pull the comments. It would really be an easy sql statement and then the matter of looping through the result set.
Yes, those other pages do have access to the WP functions. (but there is no "Loop" since there is no WP post or page displayed)
However what I need is not just to pull comments, but also to enter comments for those other pages. What I noticed is that in WP database each comment is associated with a post ID. The pages created by this other application do not have a WP post ID.