Choosing templates for Pages using "alternate themes" is a situation I had not even thought about when I designed the plugin.
I'll need to investigate that before I can comment on the feasibility of expanding the plugin to handle that in Create New Page and Edit Page.
For now, here are a couple of workarounds that may or may not work in your individual situation.
(1) If you always use the default Template of your Current Theme, you could make your Mobile Theme the Current Theme and use the plugin to select the regular Theme as your Alternate Theme for all but your Mobile pages. That would allow you to choose the Template for your mobile theme in Create New Page and Edit Page.
(2) The only other instant answer, which is just an idea, not something I've tested, would be to make Child Themes of your Mobile Theme, each Child using a different Template as its default. You would then have to use the plugin to set which Child Theme (i.e. - which Template) to use for each Page.
I'll respond here in the next 24 hours once I've had a chance to research what it would take to allow the selection of Templates for an "Alternate Theme".