I agree with you Brett, but in many ways I think that is how they want it. Alow me to try to explain why:
Link Pop generally works on all links - internal as well as external. Link Pop gives variable credence and value to a link according to the 'quality' of that link. A link from a higher ranked page for example counts more than one from a low-ranked page or a page ranked for totally unrelated terms.
So if a link grants populaity only to the specific page that receives it then the sites own internal links will pass on the benefit to a lesser degree. I.e. the page linked to now ranks more highly itself and so becomes a higher quality page when determining the value of its own links to other pages.
If it granted a benefit at the domain level the SEs would soon be stuffed with lousey results where a site with 10,000 pages of total junk ranked highly simply because just one page out of the 10,000 was extremely popular to link to.
This would result in Tripod.com, Geocities.com and Angelfire.com being the top ranked sites for hundreds if not thousands of keywords totally unrelated to hosting free space.
Aiming link pop benefits at the specific URL is simply an easier and safer method to control and to avoid irrelevant results.