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and here the quick answers :)

-The *only* way to enable those again would be to recompile, right ?
yep.

- this "JACK Latency support " must be enabled for your new "Audio recording latency compensation" thingie, ok ?
not necessarily, you still get a fixed buffer-size in length of latency compensation as default.

- "LV2 Plug-in GTK UI support disabled" does that mean anything for a KDE user ? How can I test that I have "LV2 Plug-in QT UI support" enabled, any fancy interface plugin advice ?
you need to have libgtk2-dev(el) et al. packages installed at the time you configure/compile it again.

- "VeSTige header support enabled." Is that enough to run VST plugins ? Not that I would want to, just asking.
yes its enough, although you'll miss some VST plugin features only supported through the official Steinberg VST-SDK.

cheers