Assessing multi-output bioenergy with carbon capture and storage (BECCS) systems requires methodological choices that can strongly influence the estimated environmental and climate benefits. This study (rooted in NET-Fuels H2020 project) evaluates an integrated Thermo-Catalytic Reforming (TCR) and Bio-Electrochemical Methanation (BEM) pathway that converts biomass residues into biomethane, biochar, and co-products. Two complementary frameworks are applied: attributional Life Cycle Assessment (LCA) and greenhouse gas (GHG) accounting aligned with the Renewable Energy Directive (RED III). The analysis examines the influence of assessment perspective (process- versus product-oriented), co-product allocation methods, and RED III GHG accounting on the environmental performance of the system. Environmental impacts are assessed using EF 3.1 indicators, while GHG chain emissions are quantified and benchmarked against RED III reference values. Results show that both functional unit selection and allocation approach affect burden distribution and the process carbon intensity. Accounting for biochar carbon sink substantially improves climate performance and can lead to net-negative GHG emissions under certain conditions. The study highlights key methodological considerations for harmonizing LCA and RED III assessments of emerging BECCS technologies, supporting their development and potential policy evaluation.