The most logical approach would seem to be to assume more thermal growth of the pump than motor, similar to your logic. Since often motor is more easily-moved than pump (piping constraints), it would make sense to initially set the motor high.

Of course any calculations you do using thermal coefficient of expansion and estimated temperature difference can be way off.  Best approach is to take actual measurements of alignment changes between hot and cold using Ludeca's permalign or similar equipment.  

ChipBurton,

The conclusion to your question is dependent on many factors:

1) What is feedwater temperature?  It is not unusual to have temperatures anywhere from a little over 100 DegF to 200 to 300 DegF or higher?

2) What is pump design? Radial split or horizontal split casing?

3) Is pump centerline or base mounted?

4) You may want to check with your maintenance personnel as to how they decided to set the difference in elevation?  Maybe they have some good rationale for this setting.

5) I generally don't like rules of thumb for such settings, since there are so may possible variations.

Motor thermal growth should be available from the motor manufacturer
We pump cold water with some 600 kW motors and have to align the motor low, but if you are pumping hot water then the pump will grow too.

Worlds Best practice is an educated guess at first then re-align when the unit is hot.  A bit of a hassle at first but t hen the knowledge is there forever!!!!