Phil, one alternative may be to increase the amount of solder paste  for SMD
joints to compensate for the via volume that sucks up the solder during
secondary reflow (wave solder phase). 

The  masking of vias on the  bottom side with a solder mask can create '' via
corrosion problem' by traping the flux and or cleaning residues. This has
been observed in the field. The solder mask was finally removed from the vias
to fix the field corrosion problems. That happened at my previous employer. 

Another thing to note is that when vias are masked, air is trapped in the via
after paste print and can not escape during SMD reflow. Contact me if you
want to discuss further.

Pratap Singh
RAMP Labs
512-255-6820