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I took a look at the paper and would contend that it is a typo. I would assume he just copy-pasted the equation - for it is exactly the same for the two factor model cf. eq (157) and eq (41) If you follow his reasoning and his notation it would make no sense to use the observed sample variance. He always denotes the variace by $\sigma^2$ and the ...
In fact you can calibrate $\theta(t)$ piecewise constant and $\alpha$ and $\sigma$ to bond prices only. You don't need the swaption prices in mM. If you let $\sigma(t)$ depend on $t$ (this is called the generalized Hull-White model) then you need information about the options market. For the model as you write it you don't necessarily need MC to calculate ...