The residential, commercial, utility single owner and utility IPP financing options in SAM are for projects that are developed, owned, and operated by a single entity. There are no explicit inputs for developer fees. Your approach to modeling developer fees seems like a good one, and should give you reasonable results.
The utility partnership flip and utility sale leaseback financing options are for projects with two partners, and do include an input on the Financing page for the development fee.
In general, we have tried to make SAM's financial models flexible enough model a wide range of projects, but not so complicated that they are impossible to use. Things like a developer fee, or inverter replacement for a PV project, could be more accurately modeled with more inputs, but we think can be adequately modeled with existing inputs.
We would like to hear more suggestions like this (and responses to this one) -- if there is enough interest in adding an input, and we think we can make it work in the user interface, we would be happy to do so.
Thanks,
Paul.