This work studies the significance of the lightcurve intrinsic variability in the numerical modeling of contact binaries. Using synthetic light curves we are showing that the starspot-based intrinsic variability increases the apparent mass ratio by Δq=5%. For systems with orbital period P>0.3d the effect of intrinsic variability averaged over long time cancels each other out with the Kepler Mission-like phase smearing. Further, we analyse 47 totally eclipsing Kepler Mission contact binaries. We found a sharp cutoff of the intrinsic variability at P = 0.45 d. With the light curve numerical modeling and observational relations we derive physical parameters of the 47 systems. At least 53% of binaries have a possible third companion. 21 binaries show the O`Connell effect in the averaged phase curve. 19 of them have a primary maximum lower than the secondary, suggesting a stationary dark region on the trailing side. Using the P = 0.45 d cutoff we propose a new approach on the Period-Color relation. The only parameter correlating with the magnitude of the intrinsic variability is the apparent effective temperature ratio. We conclude that instead of describing the system parameters, the A/W-subtype division should be applicable only to the lightcurves, as a tentative phenomenon.