1. Only a few methods are obfuscated
Spices.Obfuscator evaluation hasn't functionality limits, just marks obfuscated assemblies by special attribute. Probably you've used Default obfuscation mode to obfuscate your assemblies. Please see the Your first Spices.Project for obfuscation video-tutorial that helps you to familiarize with Spices.Obfuscator.
2. I cannot pass any flags
Seems it is related to the first question.
3. My assembly is signed by a password protected .pfx file. I see no way to specify a password for the pfx. Also I am not sure if you require snk only?
Currently Spices.Obfuscator doesn't automatically support .pfx files but you can use ObfuscationEvents to resign your assembly with .pfx file.
See the How to resign my assemblies by using .pfx file topic for more details.