That is exactly what they have: screamer engines updated and ready. Actually according to Guareschi they have three types of engine (I assume a screamer and two different firing orders of big bang) that are switchable any moment at the rider's request.
As regarding Stoner asking for a more tractable engine, that's exactly what happened. It's all on record. As it is on record that it was Hayden and him, together, choosing the big bang engine over the screamer for 2010, after they both tested it... There was no manipulation there, unless they hypnotized both their riders
For testing, they do have Battaini testing full time at Mugello -- and it is true that Battaini is mainly working for Rossi-2011 now. The idea of using Stoner for developing a bike for Rossi sounds risky, seen the very personal riding style and peculiar setup preferences Stoner has.
Very interesting. Have they had the screamers ready to go all year? Was the engine durability aspect which admittedly may have all been speculative as I don't recall any comment actually from ducati just that (as in speculative)? I am not sure the engine was the major problem for stoner though, but rather the new front forks, and he seems to have come up with some sort of solution of his own after reverting to the old forks. One thing burgess has definitely been quoted correctly as saying is that it took yamaha a lot of testing to get their front forks right, and this is presumably something that could be transferred to ducati.
I agree with you about it being possibly ill-advised to have stoner test for rossi