ya, that's right, good point. For complete GHGP inventory reporting, customers need to estimate employee commuting separately (and we're happy to help with that; it's usually a pretty straightforward calculation, though gathering the employee info takes some doing).
Setting the GHGP aside, my own personal opinion about how we interpret GHGP data is that it's important to make a clear distinction between upstream emissions and downstream emissions. For example, 'use of sold products' (Category 11) is also not something you can determine from spend data. But I'd argue that 'use of sold products' is a very different thing than upstream emissions (even though they're all lumped under Scope 3).
Commuting is a less clear-cut case, but I think of commuting (that is paid for by employees) as more of a downstream emissions category.
We wrote up some notes on this here: https://bend.green/faq/downstream-emissions
