There's a reason we have lots of tiny configuration panels instead of a few huge ones, and that reason is that not everyone has a 1600×1200 desktop. 640×480 is still a viable resolution for running Windows (and indeed it's still the default if you start up in safe mode), so it's still a resolution we care about.
Accordingly, the PuTTY configuration box, and the PuTTYgen control window, are deliberately kept just small enough to fit comfortably on a 640×480 display. If you're adding controls to either of these boxes and you find yourself wanting to increase the size of the whole box, don't. Split it into more panels instead.