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.
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