I'm not saying that its "best" to finish with a flat coat over the Alclad II...I'm just saying that I haven't had problems doing it. I think that its best not to put a flat coat over the Alclad II if you can do it that way. I think, ideally, it would be best if you could figure out how to finish the spine and tail without coating the NMF.
For example, you could use post-it-notes or something that has very low tack to mask off the NMF so you don't run the risk of lifting any decals. Then use a gloss coat that you can spray through the airbrush so you have better control over the spray. Don't use the canned stuff.
Another better method you could try is to use a steady hand and brush some Future onto the areas that need the semi-flat. One thin coat of Future will not look too glossy. This might be the best way to go about it. I just used this technique on an F/A-18E that I built recently. The spine of the fuselage needed to be glossy black while the the rest needed to be flat grey. I could't mask with all the decals so I just brushed on the Future and it looked really good.