Extended stem normally applied whenever the valves are somehow not in a close proximity with the Operator location when he's about to operate the valve (i.e. valve located under water / under ground, too hot of pipeline/valve temperature, potential toxic release / considered as confined space, etc.). I believe disadvantages of this are only Plant ergonomic layout (shall effected due to some extended bonnet may obstruct gangway, etc.) and also if not calculated prior, the extended bonnet may suffer bent due to moment by actuator or additional heights --> thus might get stuck.
Extended Bonnet has a different meaning. Its function is to "isolate" the gland from the high or low temperature zone so as to maintain integrity of the stem seal and the operation of the valve.
Best practice definition of low & high temperature should extended bonnet applied is normally depends on Plant's best practice. below -50 deg C and Or above 200 deg C may requires bonnet extension.
Yes, Graphite (standard) could withstand lower or higher then that, however shall it requires to operate the valve during emergency (before gland packing could establish itself towards ambient temperature of -20 up to let say 100 deg Celcius) experiences shows that this repetitive actions will disrupt gland integrity. Then of course leaks or burst through "stem".