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re. what is the purpose of these MIDI programs, are they for hardware devices?
yes, but not only for hardware devices--some instrument plugins may have a "programs" menu where you can switch or select one of its programs (or presets) either directly on the GUI or via a MIDI bank-select + program-change channel message; most few DSSI plugins have this ootb. it's also common to find this on many VSTi; you can also find this programs interface on LV2 plugins, especially the distrho supplied ones.

re. 1)... "shift-click" or "ctrl-click" on the plugin for the alternative window ("properties" or "edit")
might think about it, yeah :) [UPDATE: done on svn trunk rev.3842+ (aka. qtractor 0.6.1.8+)]

re. 2)... is there a way to trigger the reloading of the presets manually without reloading the whole session?
LV2 presets are stored in its own external namespace (files-system) and get re-enumerated only on special occasions during qtractor run-time: the whole LV2 inventory is only refreshed on session (re)start/open, so any new LV2 presets that are created during one current qtractor session are only "seen" after a next (re-)start or session opening--just an "inconvenience" indeed, but hardly a showstopper ;)

re. 3)... Is there a way to disable this red rectangle in Qjackctl systray icon? I know I have xruns, no need to blink:)
nope. there isn't any but you can clear it up on demand: middle-click on the main window or system tray icon to reset xrun stats ;)

hth.
cheers