"What procedures do you or your airline use to ensure that QNH or QNE are set through transitions?"
I guess this would depend on the degree of sophistication of your aircraft. With glass cockpits, a quick software change can add bells and whistles and flashing lights to the cockpit environment as you near or pass through transition (without presetting your altimeters). Modern Flight Management Computer databases invariably have transition alt/ht information for various airports and this data is used, for example, by the EFIS/EICAS displays on our airline's 747-400s to generate messages/visual warnings if the pilots forget to set their altimeters.
Perhaps this info is of no help to you and your particular situation, but....
Rgds.
Q.