There should be a workaround, if it happens to work with 4.0.7 pad capabilities. I have tested this basic idea only with v5 nightlies, but it should be doable in v4.
Create a footprint with a through-hole pad which you will use as the net tie footprint and instead of a via. The pad has only the top layer. Set the dimensions which fit your case.
On the bottom layer create a non-pad copper area around the hole so that it reminds a pad ring. Maybe it can be a polygon. It should cover the hole or overlap it. In v5 it's possible to create a graphical circle and put it on a copper layer. This non-pad copper area is the actual tie.
Create the pad number two on the bottom layer. In v5 (the latest code) it's possible to create a graphical circle (a ring) and make it a pad. In v4 it can be done with a group of pads which all have the same pad number, positioned so that they form a ring. Make as many as you need. It must be around the non-pad copper area, overlapping it a tiny bit.
You have to set the dimensions and clearances so that there will be no DRC errors. The footprint and pads can probably have very small clearances. There are two problems. The first is that zone filling uses the through hole's net class clearance - not the zone's, pad's or footprint's clearance. Therefore the distance between the bottom outer pad's outer edge and the hole's edge must be larger than the net class clearance of the through hole pad's net.
The second problem is that zone filling avoids the non-pad copper area of a footprint. There the zone's clearance is used. So, either the zone's clearance must be small or the bottom outer pad must be wide enough.