This question makes reference to section 8.4 - Application to performance measure - of the 2007 publication "Performance Measurement for Traditional Investment" by Véronique Le Sourd. You can find the paper here.
In her article, the author states that the implementation of factor models is carried out in two stages (if I understand correctly, she refers to the Fama Macbeth methodology). First, betas are estimated by means of a series of time series regressions of asset returns (one for each asset $i$) on factor returns:
$(1)$ $R_{it} = \beta_{i0} + \sum_{k=1}^K\beta_{ik}F_{kt}+\epsilon_{it}$
Then, lambdas are estimated running a cross-sectional regression at each date $t$:
$(2)$ $R_{it} - R_f = \hat\alpha + \sum_{k=1}^K\hat\beta_{ik}\hat\lambda_{kt}+\zeta_{it}$
After calculating the average risk premiums as:
$(3)$ $\lambda_k = \frac{1}{T}\sum_{t=1}^T\lambda_{kt}$
She states that fund performance is given by:
$(4)$ $\alpha_i = \bar{R_i} - \bar{R_f} - \sum_{k=1}^K\hat{\beta_{ik}}\lambda_k$
What is not clear to me is why one would estimate alpha as in equation $(4)$ instead of simply considering as alpha the estimate of the coefficient called $\beta_{i0}$ in equation $(1)$.
For instance, if I were to employ the Fama-French three-factor model to estimate alpha, should I follow the procedure above or simply estimate alpha as the intercept of the following regression?
$R_{it} - R_{ft} = \alpha_i + \beta_i(R_{mt}-R_{ft}) + s_iSMB_t + h_iHML_t + \epsilon_{it}$