Sure you can do that. the only problem is that they don't seem to have boxes or bags for carryout, so it's a long way to walk carrying a plate or a tray.
I did the reverse of this on my last trip and didn't have any problems. It worked out good because pizzafari opened before flame tree.
We actually did this. Our family of 6. 3 wanted Pizzafari, and 3 wanted Flametree. So I stayed with the 3 of the kids, ordered their food, while DH and oldest son 19 went to Flametree. It really wasn't far, and I can tell you that my food was still hot when they arrived. So hot that I had to wait to eat the baked beans. So very doable without a lot of trouble.
Restaurantosaurus "may" be a little shorter walk.
Personally,I just couldn't eat my FTB ribs without enjoying this view from the "Discovery River pavilion"(One of the best views in WDW).
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I think someone should at least order part of a meal at Pizzafari if you're planning on taking up a table there. It just seems wrong to go sit at a random table somewhere without ordering.
They are both owned by WDW so I see no problem. It isn't like getting food at Wendy's and taking it to McDonald's.