The growing deployment of Sustainable Aviation Fuels (SAFs) collides with an aviation greenhouse gas (GHG) accounting landscape that remains largely fossil-baseline- and tank-to-wake (TTW)-focused. Operational calculators used for corporate reporting and disclosure—such as Google’s Travel Impact Model, IATA CO₂ Connect, the ICAO Carbon Emissions Calculator, ATP-DEC and the UK DEFRA factors—generally assume 100% conventional jet fuel and offer little structural treatment of SAF. This study quantifies well-to-wake (WTW) CO₂-equivalent emissions for ten commercial flights operated with certified SAF blends and documented pathways, including hydroprocessed esters and fatty acids (HEFAs), Fischer–Tropsch fuels and power-to-liquid e-fuels. Using flight-specific fuel uplift, blend share and aircraft data combined with ISO 14067/14083-consistent life-cycle assessment, the analysis derives WTW intensities per flight, per seat-kilometre and per passenger-kilometre. These empirical results are then compared with estimates from the above calculators, each run under its native distance uplift, passenger-and-cargo allocation and non-CO₂ conventions. The comparison decomposes discrepancies into contributions from the TTW versus WTW scope, treatment of SAF, non-CO₂ assumptions and allocation rules. In addition to climate change impact, the work screens a limited set of further impact categories (such as land-use change, eutrophication potential and water use) to explore trade-offs for SAF produced from dedicated biomass versus waste-based feedstocks. Building on the findings, the paper proposes a minimal, auditable protocol for integrating SAF into existing tools—explicit TTW/WTW disclosure, transparent non-CO₂ options, pathway- and blend-specific WTW factors and book-and-claim rules compatible with SAF certificates—aimed at making SAF deployment visible, comparable and verifiable in Scope 3.6 business-travel accounting.