should commuting be included in emissions

Commuting falls under scope 3, not under scope 1 or 2

Yes, commuting counts, but not under scope 1 or scope 2. The GHG Protocol places employee commuting in scope 3, category 7 ("employee commuting"). That is the category for indirect emissions that arise outside your own business operations, but are nonetheless a result of how your business operates. Employee cars or public transport cards are not owned by the company and fuel is not purchased by the company — which is why this never falls under the direct emissions of scope 1 and also not under the purchased energy of scope 2.

For the VSME-basic module of EFRAG, scope 3 in the basic reporting is not mandatory broken down by category. Many customer formats therefore only ask for the total emissions in the value chain, without asking separately about commuting. If you do receive that question separately, an estimate based on known data (number of employees, average travel distance, mode of transport) is the standard answer — as long as you state that it is an estimate and not a measured value. If you do not have that data, then "no" or "unknown" is the honest answer; presenting an estimated figure without any underlying data is not defensible towards your customer.

Where that is in the GHG Protocol structure

The scope structure of the GHG Protocol works with three categories: scope 1 for direct emissions from own sources, scope 2 for indirect emissions from purchased energy, and scope 3 for all other indirect emissions in the value chain. Commuting is specifically named within that as one of the fifteen standard categories of scope 3, alongside for example business travel and emissions from suppliers. The fact that it is separately named is precisely why customers sometimes ask about it separately, even though it falls under the same scope 3 that you already as a total figure for the value chain provide.