Hi

JTV-59 and JTV-89 with POD HD500 or POD HD Pro and DT-50 212 here

1. The JTVs can send the magnetic pickup output signal and the modelled signal over the Variax Digital Interface connection separately on Variax Channel 1 for the models and Variax Channel 2 for the mags.  On the guitar, just press the model selection switch and then in a two channel patch you can blend. cross-fade or just use one or other VDI input channel
2. Yes - this is a bit of a limitation for the HD500 and the POD HD Pro, but it can be worked around quite easily to give a satisfactory result and depending on what you are trying to achieve you might want to consider something like the H&K Red Box DI box with cabinet modelling or the inexpensive Behringer Ultra-GI GI100 DI box with cabinet modelling to give the PA option a suitably voiced option.  However, yes, you can certainly use the FX loop as a suitable 'send' for getting an uncoloured acoustic signal out to the PA.  You might still want a DI box for this depending on the distance between the HD500 and mixing desk. There are various ways of muting the normal signal path post FX Loop so your main on-stage amp remains silent during acoustic sections I have done this.  You might also be able to do what you want by panning at the HD500 mixer block stage.

Nick