I think the last thing we need to worry about is canon in an IDW comic, a comic which is after all licensed only for America (as I understand it), there is no need what so ever to consider any IDW comic anything more than you want it to be, be it canon or not.
I've seen similar sentiments at Gallifrey Base; because this isn't a Panini product, it can't possibly "count." Never mind that this crossover would have to go through the exact same approval process
that Panini's own Doctor Who
comics go through.
That said, indications are right now that this project will be the first IDW Doctor Who
product available officially in the UK.