The aim of this work is to study the possible effects and biases on the radius constraints for rotation-powered millisecond pulsars when using Thomson approximation to describe electron scattering in the atmosphere models, instead of using exact formulation for Compton scattering. We compare the differences between the two models in the energy spectrum and angular distribution of the emitted radiation. We also analyse a self-generated, synthetic, phase-resolved energy spectrum, based on Compton atmosphere and the most X-ray luminous, rotation-powered millisecond pulsars observed by the Neutron star Interior Composition ExploreR (NICER). We derive constraints for the neutron star parameters using both the Compton and Thomson models. The results show that the method works by reproducing the correct parameters with the Compton model. However, biases are found in both the size and the temperature of the emitting hotspot, when using the Thomson model. The constraints on the radius are still not significantly changed, and therefore the Thomson model seems to be adequate if we are interested only in the radius measurements using NICER.