Scientific and engineering verticals often suffer from data scarcity and strict executability requirements: models must generate not only fluent text, but also syntactically valid, tool-compilable scripts. We present a schema-first alignment framework for building compact, executable domain-specific LLMs in low-resource settings. The framework integrates three core components: (i) large-scale synthetic QA data generation from expert documentation to instill foundational domain knowledge; (ii) a code-centric IR->DPO workflow that converts verified tool decks into interpretable intermediate representations (IR), performs equivalence-preserving diversification, and constructs preference pairs to directly optimize instruction compliance and code executability; and (iii) a controlled evaluation of Retrieval-Augmented Generation (RAG), showing that while RAG benefits general LLMs, it can marginally degrade the performance of already domain-aligned models. We demonstrate the framework by instantiating TcadGPT for semiconductor Technology Computer-Aided Design (TCAD). Using 1.5M synthetic QA pairs and an IR-driven DPO dataset, TcadGPT attains 85.6% semantic accuracy and an 80.0% syntax pass rate on SDE executability tests, substantially outperforming state-of-the-art general LLMs such as GPT-4o. To probe portability beyond TCAD, we apply the same recipe to the open-source FEM solver Elmer, observing consistent improvements in script-level success rates over general-purpose baselines. All datasets, benchmarks, and code (including P1, P2, and IR->DPO) are released for reproducibility. Together, these results suggest that the proposed framework provides a robust and reproducible path toward executable LLMs in specialized, data-scarce professional domains.