In this paper, we propose two novel physical layer aware adaptive network coding and coded modulation schemes for time variant channels. The proposed schemes have been applied to different satellite communications scenarios with different Round Trip Times (RTT). Compared to adaptive network coding, and classical non-adaptive network coding schemes for time variant channels, as benchmarks, the proposed schemes demonstrate that adaptation of packet transmission based on the channel variation and corresponding erasures allows for significant gains in terms of throughput, delay and energy efficiency. We shed light on the trade-off between energy efficiency and delay-throughput gains, demonstrating that conservative adaptive approaches that favors less transmission under high erasures, might cause higher delay and less throughput gains in comparison to non-conservative approaches that favor more transmission to account for high erasures.