How to fill pad with polygon pour
Couple of ways to do this either on an as-needed basis or globally. On every design I create a rule as seen in the photo.  Then, for example, if you want just a select number of pads (on a net that I may not want ALL pads flooded for that net) flooded with copper I will create a small polygon (to place on top of the parent polygon) just big enough to cover the pad in question and name this polygon "Pin Flood".

Or, if you want ALL pads flooded for ALL nets then just change the default "PolygonConnect" to Connect Style==>Direct Connect.

And for lesson #2. You can also create a Pad Class as you see in this photo.


Then create a new rule in Polygon Connect that you see in this photo.

This method is a bit more portable and easier to manage.

EDIT ...and as Chris Stratton points outs above. Flooded copper on TH pads may complicate soldering in terms of proper wetting of the solder fillet. One can always change the rule set from "Direct Connect" to "Relief Connect" and fatten-up the thermal ties.