That's an aesthetic preference you should really take up with Moveable Type's template designers. They intend (in the v2.6661 and 3.0 templates, anyway) for these windows to be popup windows, and the templates are designed as such. Accordingly, the restriction level would show them as popups. To me, that's seems very much like the right thing to do, regardless of one's preference about whether or not it's a good use of a sized window or not.
== More comments from Jesse ==
When I check "Force links that open in new windows to open in: a new tab", I expect it to apply to all such links, not a random-seeming subset of those links. I think the same is true for most users who check that option.