Effective trajectory generation is essential for reliable on-board spacecraft autonomy. Among other approaches, learning-based warm-starting represents an appealing paradigm for solving the trajectory generation problem, effectively combining the benefits of optimization- and data-driven methods. Current approaches for learning-based trajectory generation often focus on fixed, single-scenario environments, where key scene characteristics, such as obstacle positions or final-time requirements, remain constant across problem instances. However, practical trajectory generation requires the scenario to be frequently reconfigured, making the single-scenario approach a potentially impractical solution. To address this challenge, we present a novel trajectory generation framework that generalizes across diverse problem configurations, by leveraging high-capacity transformer neural networks capable of learning from multimodal data sources. Specifically, our approach integrates transformer-based neural network models into the trajectory optimization process, encoding both scene-level information (e.g., obstacle locations, initial and goal states) and trajectory-level constraints (e.g., time bounds, fuel consumption targets) via multimodal representations. The transformer network then generates near-optimal initial guesses for non-convex optimization problems, significantly enhancing convergence speed and performance. The framework is validated through extensive simulations and real-world experiments on a free-flyer platform, achieving up to 30% cost improvement and 80% reduction in infeasible cases with respect to traditional approaches, and demonstrating robust generalization across diverse scenario variations.