You can still have a separate flight NRT-ITM/KIX or vice versa at either end. It can even save you some money and since the trip from NRT to Tokyo Station takes with NEX an hour alone, it can save you some time too.

If you are looking into rail pass for its convenience then don't underestimate the Nozomi restriction. It is little pity that many visitors don't get full experience of the efficiency of the Japanese Shinkansen network because of that. Buying tickets is simple in Japan and for local train trips you can have pre paid IC card which is again more convenient because with rail pass you have to find a manned gate and show it there. I just did a trip in Japan with JR Pass and especially west of Osaka I found it little irritating that quick non-Nozomi connections were not very frequent when there was still multiple Nozomis per hour. Before I had travelled without any rail pass and with regional rail pass that was good on all trains and the overall experience was different.

Many seem to think JR Pass is almost compulsory if visiting Japan but my opinion is that it is not worth is unless you save some real money or you know the restrictions won't affect you (Nozomi and Mizuho Shinkansens operate only west of Tokyo in Kyushu, Sanyo, and Tokaido Shinkansens). And if money savings are important you can save even more by staying in one area.