I'm already have working solution for windows. You can find it in my finished projectcs (https://www.freelancer.com/projects/C-Sharp-Programming/Google-Chrome-Secure-preferences/).
It is console application which can change Chrome's homepage and search engine with specified as arguments (homepage url, se url, se name, se favicon, ...).
It is written using Chromium source codes, compiled with MS VC++ 2013 wihout any 3rd party dependencies. This app also correctly rebuild Chrome's preferences digital signature, so Chrome don't display message about setting was changed.
I can send demo app which change Search engine to DuckDuckGo.com.