Channel coding from 2G to 5G has assumed the inputs bits at the physical layer to be uniformly distributed. However, hybrid automatic repeat request acknowledgement (HARQ-ACK) bits transmitted in the uplink are inherently non-uniformly distributed. For such sources, significant performance gains could be obtained by employing joint source channel coding, aided by deep learning-based techniques. In this paper, we learn a transformer-based encoder using a novel "free-lunch" training algorithm and propose per-codeword power shaping to exploit the source prior at the encoder whilst being robust to small changes in the HARQ-ACK distribution. Furthermore, any HARQ-ACK decoder has to achieve a low negative acknowledgement (NACK) error rate to avoid radio link failures resulting from multiple NACK errors. We develop an extension of the Neyman-Pearson test to a coded bit system with multiple information bits to achieve Unequal Error Protection of NACK over ACK bits at the decoder. Finally, we apply the proposed encoder and decoder designs to a 5G New Radio (NR) compliant uplink setup under a fading channel, describing the optimal receiver design and a low complexity coherent approximation to it. Our results demonstrate 3-6 dB reduction in the average transmit power required to achieve the target error rates compared to the NR baseline, while also achieving a 2-3 dB reduction in the maximum transmit power, thus providing for significant coverage gains and power savings.