Multimodal Large Language Models (MLLMs) rely on multimodal pre-training over diverse data sources, where different datasets often induce complementary cross-modal alignment capabilities. Model merging provides a cost-effective mechanism for integrating multiple expert MLLMs with complementary strengths into a unified model. However, existing model merging research mainly focuses on post-finetuning scenarios, leaving the pre-training stage largely unexplored. We argue that the core of MLLM pre-training lies in establishing effective cross-modal alignment, which bridges visual and textual representations into a unified semantic space. Motivated by this insight, we introduce the post-alignment merging task, which aims to integrate cross-modal alignment capabilities learned from heterogeneous multimodal pre-training. This setting introduces two key challenges: cross-domain parameter interference, where parameter updates learned from different data distributions conflict during merging, and layer-wise alignment contribution disparity, where different layers and projectors contribute unevenly to cross-modal alignment. To address them, we propose \textbf{PivotMerge}, a post-alignment merging framework for cross-modal projectors. PivotMerge incorporates two key components: Shared-space Decomposition and Filtering, which disentangles shared alignment patterns from domain-specific variations and suppresses conflicting directions, and Alignment-guided Layer-wise Merging, which assigns layer-specific merging weights based on differing alignment contributions. We construct systematic CC12M-based post-alignment merging scenarios for evaluation. Extensive experiments on multiple multimodal benchmarks show that PivotMerge consistently outperforms existing baselines, demonstrating its effectiveness and generalization ability.