Microwave linear analog computer (MiLAC) has emerged as a promising architecture for implementing linear multiple-input multiple-output (MIMO) processing in the analog domain, with radio frequency (RF) signals. Existing studies on MiLAC-aided communications rely on idealized channel models and neglect antenna mutual coupling. However, since MiLAC performs processing at RF, mutual coupling becomes critical and alters the implemented operation, not only the channel characteristics. In this paper, we develop a physics-compliant model for MiLAC-aided MIMO systems accounting for mutual coupling with multiport network theory. We derive end-to-end system models for scenarios with MiLACs at the transmitter, the receiver, or both, showing how mutual coupling impacts the linear transformation implemented by the MiLACs. Furthermore, we formulate and solve a mutual coupling aware MiLAC optimization problem, deriving a closed-form globally optimal solution that maximizes the received signal power. We establish the fundamental performance limits of MiLAC with mutual coupling, and derive three analytical results. First, mutual coupling is beneficial in MiLAC-aided systems, on average. Second, with mutual coupling, MiLAC performs as digital architectures equipped with a matching network, while having fewer RF chains. Third, with mutual coupling, MiLAC always outperforms digital architectures with no matching network. Numerical simulations confirm our theoretical findings.