setup.py is not tied to scrapy/scrapyd; it is just a standard mean of creating setuptools package. Users could customize it to include data files or change the metadata.

Please correct me if I'm wrong, but the template is hardcoded in scrapy/scrapyd code. It is not a good idea to change the installed Scrapy version for multiple reasons: template can be shared with other scrapy projects, scrapy updates will overwrite the changes, these changes won't be in VCS, etc.

Multiple deploy targets feature looks reasonable, but I haven't dug in to check how it iteracts with other scrapy/scrapyd parts - sorry, I don't have suggestions now.