We analyze the early X-ray flares in the GRB flare-plateau-afterglow (FPA) phase observed by Swift-XRT. The FPA occurs only in one of the seven GRB subclasses: the binary-driven hypernovae (BdHNe). This subclass consists of long GRBs with a carbon-oxygen core and a neutron star (NS) binary companion as progenitors. The hypercritical accretion of the supernova (SN) ejecta onto the NS can lead to the gravitational collapse of the NS into a black hole. Consequently, one can observe a GRB emission with isotropic energy E-iso greater than or similar to 10(52) erg, as well as the associated GeV emission and the FPA phase. Previous work had shown that gamma-ray spikes in the prompt emission occur at similar to 10(15)-10(17) cm with Lorentz Gamma factors Gamma similar to 10(2)-10(3). Using a novel data analysis, we show that the time of occurrence, duration, luminosity, and total energy of the X-ray flares correlate with E-iso. A crucial feature is the observation of thermal emission in the X-ray flares that we show occurs at radii similar to 10(12) cm with Gamma less than or similar to 4. These model-independent observations cannot be explained by the fireball model, which postulates synchrotron and inverse-Compton radiation from a single ultrarelativistic jetted emission extending from the prompt to the late afterglow and GeV emission phases. We show that in BdHNe a collision between the GRB and the SN ejecta occurs at similar or equal to 10(10) cm, reaching transparency at similar to 10(12) cm with Gamma less than or similar to 4. The agreement between the thermal emission observations and these theoretically derived values validates our model and opens the possibility of testing each BdHN episode with the corresponding Lorentz Gamma factor.