We set 1013 when cleared to a FL and QNH when cleared to and altitude. Both main altimeters are set together and the STBY can be used for "passing" reports to ATC if required.
The danger of waiting until passing transition is that it gets missed (distracted by someting else perhaps?). Take BHX Sids as an example. Transition altitude of 4000' and a SID block of FL60. QNH is 980 so you "wind on" about 990 when you pass 4000', hence you have 1000' to go when you may have thought 2000' to go.
Also bear in mind that it depends on how your aircraft works. Your SOP's should take into account that perhaps the Right Autopilot gets it's data from the Right ADC. The other A/P's might get their data from the Left ADC. No good having the R A/P engaged if the R altimeter is not set appropriately!
The more you dig, the more complicated it gets.
