What Changes Take Place When Installing A Custom Launcher eg Nova To A Rom? If I install a custom launcher eg Nova on Stock Android 4.4.3, what inherently changes ?

Similarly if I were to then install a custom rom eg Paranoid Android, are the benefits gained from installing it then overshadowed or "lost" if I were to then install Nova launcher ?

To clarify wouldn't the experience of Stock Android with Nova and Paranoid Android with Nova be very similar if not identical ?
If you install a alternate launcher, the first thing you'll see is a difference in how the home screen, widgets, (maybe lockscreen if it has support for that), and the app drawer appears and works.

AFAIK that's the only changes you'll see from changing the launcher regardless of what ROM you use.

But one thing's for sure - depending on which ROM you get, the experience will change very little or a lot.