Visible light communication (VLC)-based beacon systems, which usually transmit identification (ID) information in small-size data frames are applied widely in indoor localization applications. There is one fact that flicker of LED light should be avoid in any VLC systems. Current flicker mitigation solutions based on run-length limited (RLL) codes suffer from reduced code rates, or are limited to hard-decoding forward error correction (FEC) decoders. Recently, soft-decoding techniques of RLL-codes are proposed to support soft-decoding FEC algorithms, but they contain potentials of high-complexity and time-consuming computations. Fortunately, non-RLL direct current (DC)-balance solutions can overcome the drawbacks of RLL-based algorithms, however, they meet some difficulties in system latency or inferior error-correction performances. Recently, non-RLL flicker mitigation solution based on Polar code has proved to be an optimal approach due to its natural equal probabilities of short runs of 1's and 0's with high error-correction performance. However, we found that this solution can only maintain the DC balance only when the data frame length is sufficiently long. Accordingly, short beacon-based data frames might still be a big challenge for flicker mitigation in such non-RLL cases. In this paper, we introduce a flicker mitigation solution designed for VLC-based beacon systems that combines a simple pre-scrambler with a Polar encoder which has a codeword smaller than the previous work 8 times. We also propose a hardware architecture for the proposed compact non-RLL VLC receiver for the first time. Also, a 3-bit soft-decision filter is introduce to enable soft-decoding of Polar decoder to improve the performance of the receiver.