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Health Technology Assessment (HTA) is shaped by moral (what makes a health technology desirable or acceptable, e.g., beneficence, justice), epistemological (how reliable knowledge is obtained and validated, e.g., evidence standards, uncertainty handling), and ontological (what effects and outcomes are considered real and relevant for assessment) commitments. The EU Joint Clinical Assessment (JCA), intended to harmonize relative effectiveness evaluation, embeds these commitments implicitly rather than explicitly, creating transparency and consistency issues. Critical concerns include: rigid reliance on the PICO framework privileging RCTs and quantifiable outcomes, proliferation of PICOs leading to infeasible evidence requirements, inadequate handling of multiplicity and post-hoc analyses, conflation of certainty and uncertainty, and exclusion of qualitative evidence and stakeholder input. Guidance documents, criticized for methodological weaknesses (e.g., outdated tools, poor external validity assessment, nominal p-values acceptance), further undermine epistemic robustness. These structural flaws risk producing assessments that are non-inclusive, reductionist, and epistemologically inconsistent. Future EU HTA frameworks should explicitly align on foundational commitments and integrate stakeholder perspectives to ensure transparency, scientific credibility, and ethical legitimacy.