I just happened to notice that there's a beta of PTGui Pro version 9 (http://www.ptgui.com/beta.html) available since yesterday, and after reading and getting a feel for what is involved in masking nadir shots made with the nadir adaptor it looks like it now offers this, so maybe no need to mess with alpha channels in Photoshop.

I haven't yet bought my stitching software, this looks like leaning me more to PTGui - I'll be interested to see if anyone tries this feature out, and what their feedback is.

Although my NN5 kit arrived nearly two weeks ago (thanks badders) I still haven't found any time to try it out, but I must say that I'm impressed with the build quality - it feels nice and solid.