Balok, you may find you are going to have to answer those questions yourself and post back to us. There is a thread where I asked the dev who responded a follow up question and it was never answered. So I would not hold your breath waiting for a dev to help
I would start with a fresh mod, make a small change that triggers the warning and check if things work. Start a new game with your mod, see if it impacts the intro. Then go back and see if your NPC's can move around - especially the areas you navmeshed. I could be wrong here, but from my own experience and I have edited a lot of vanilla road navmeshes and what the dev states, I don't think it's a mod breaker.
Here's the thread where this pathfinding is discussed: http://www.gamesas.com/index.php?showtopic=1384974
I can possibly use prims set to navi_cut where I add new buildings over existing navmeshes, but if simple tweaks like this are going to be a problem, my NPC’s won’t have a way to enter/exit my new stuff which will have a great impact on my mod. So I desperately need some guidance here.
From my experience, that would concern me way more than the "warning" the CK is giving. I don't know that tool at all, so I can't say if it will be a problem, but the issues I've heard about from the other tools makes me not want to use any tool atm.