I don't know how you could "create" a paradox. It can arise naturally as a consequence of time travel. In Before the Flood for example: the Doctor creates the ghost because he sees the ghost. You are saying that the Valeyard created the ghost so that the Doctor can then program his ghost...in which case, that would automatically not be a paradox since the ghost has now a point of origin.. i.e. the Valeyard. The bootstrap paradox essentially means that information/object has no defined point of origin. So that would automatically mean that most of the paradoxes we encounter in series 9 are actually not paradoxes but orchestrations of the Valeyard in order for the Doctor to survive. But in order for the Valeyard to be able to plot these things precisely, he needs to have access to this information. Where is that coming from though? From the future possibly. So maybe the Doctor dies in Before the Flood and his ghost appears. The Valeyard then uses the ghost Doctor to warn the "still alive" Doctor. But if the Doctor never died in the future, where did the Valeyard get the ghost Doctor information from? It just replaces one bootstrap paradox with another bootstrap paradox.

My explanation : Where there is time travel, you'll find a paradox. You could argue that it is present in TMA/TWF, the series 9 opener. You could even make a case for it in Husbands of River Song that the only reason he gives her the screwdriver is because he knew she had it with her in the library in the first place. The bootstrap paradox has been always around in new Who (Blink, Listen, Pandorica Opens/Big Bang to name a few) we just didn't have our attention directed to it. Although, I don't think that Heaven Sent has a bootstrap paradox at its core. That story makes sense even without the paradox.

Yes, maybe the Valeyard can sort of engineer these paradoxes but not without getting involved in paradoxes himself, IMO.