Variation analysis is a strategic task to control how dimensional and geometrical deviations, due to manufacturing processes, propagate during assembling phases. Over the years, several numerical methods have been proposed to model variational assemblies under the main hypothesis of rigid assembling parts. However, when parts deform during assembling operations, the flexibility of parts has to be considered in the model to better evaluate variations. A methodology - called SVAFEA and proposed by the same authors, to do variation analysis of compliant assemblies - has been already tested recently with respect to the TAA module of CATIA® CAD system, for a single-station case. In the present paper, SVA-FEA is used to perform the comparative analysis with TAA for multi-station assemblies. The main differences have been outlined, highlighting the key characteristics of the two simulation tools.