Hey Dave
JACK1 is definitely more reliable than JACK2, as some plug-ins (notably VST
ones) may fail to launch/run properly. But this is negligible, and not a
factor at all if your system is native.
JACK has nothing to do with "apps" code-wise unless there is a specific
compile-time config which the app needs, so there is no need to recompile
anything of that sort (Ardour, Qtractor). What usually requires
recompilation are libraries, but so far I don't know of any such
inter-related lib. For eg. you can have an older ffado and still run jack
with firewire.