Hi Carsten,
sounds a bit weird to me as well :-S
here my 2ct (actually 2GRD):
1) was always recommended in the past, as per default in ini file its UC_EX_JOB_MD=ucxj???m
2) Its always been "Automic strongly recommends installing the agent in a separate directory." No Idea why this is mentioned...
3) hmm yes.
regarding x86 (if the x86 was your point) - Yes there does exist a ucxjli3m binary as part of the 32 Bit linux agent (here from V11.2.9)

As long as I can remember job messenger binary was in lowercase letters.
cheers, Wolfgang