I don't understand. Is the Canadian regiment guarding the Queen as Queen of Canada or as Queen of the United Kingdom? The latter doesn't make sense in my opinion.
I don't know the protocol for military honors to the Sovereign in the United Kingdom, but do the regiments also use the royal standard in those occasions in addition to their own regimental colors? If so, and if the regiment is guarding the Queen of Canada, should the Queen's Canadian standard (i.e. the banner of arms of The Queen in Right of Canada) be used instead? It would be quite odd to do that on British soil.
They are certainly guarding her as part of their birthday celebrations because she is Queen of Canada. But maybe not as Queen of Canada. I suppose it does depend on if there's a technical or protocol difference.
Canadian Regiments have been Queen's Guards many times before, as have Australian, Jamaican, Gibraltarian and NZ. The only time guards have not been there because she is their Head of State is Malaysia, having been personally invited by General Sir Richard Dannat.