As research into candidate waveforms for sixth generation (6G) communication systems accelerates, chirp-based multicarrier, notably the generalized version Affine frequency division multiplexing (AFDM) have garnered increased attention. This paper introduces a novel, low-complexity channel estimation (CE) method that exploits the properties of chirp carriers in the post-coded time domain (PCTD). Initially, we derive the explicit input-output relationship under practical pulse shaping, highlighting the impact of pulse mismatch in the Affine domain. Subsequently, we analyze the inherent properties of AFDM in the Affine domain and identify the limitations of current CE techniques. As such, we present a detailed representation of single and multiple chirp carriers in the PCTD both preand post-channel transmission, with a focus on interpreting the effects of delay and Doppler shifts. Building on that, we propose a two-stage CE method leveraging the zero-padded PCTD received signal, effectively decoupling delay and Doppler components while compensating for phase selectivity and pulse shaping-induced inter-carrier interference (ICI). Our approach considers data-pilot interference levels within adaptive scenariobased frame structures, leading to a significant reduction in complexity and enhanced spectral efficiency (SE) due to minimized pilot overhead. Simulation results reflect the superiority of our proposed method over existing iterative schemes, highlighting its efficacy in improving performance in practical AFDM systems.