There are few tools that allow you to run spatially explicit Tier 1 estimations (or spatially explicit Approach 3 at any Tier). If you want to go spatially referenced, then ALU or the IPCC tool should work. If you want to go spatially explicit then the FLINT is the best bet - this will also allow you to move to higher tiers later. Note that if you have multiple changes in land use over time for a single land unit, then you may hit issues: FLINT is set up for this but other tools are not. These are all described in the GFOI methods and guidance documents. Feel free to contact me if you want more information
Sure: look at moja global (www.moja.global). All the tools I mentioned have advantages and disadvantages: you just need to decide what suits your needs best.