I think I found a solution to #1 - a quick way to set default chromium flag values to bake them into a compilation/build.
1) Set default flags to build apk: edit chrome/browser/about_flags.cc, then modify corresponding flag's feature entry so that the default flags_ui has switches::disabled/enabled_whatever, or just replace the default flags_ui with the disabled/enabled flags_ui.
Now, this will bake the desired chromium flag settings into a compiled build, however, this might cause unusual behavior even when it shouldn't (probably per flag). For example, I disabled GPU rasterization flag by default this way in a chromium-based Brave Browser Android build, the browser loads and works fine, but when I tried flipping the flag to Enabled after launching the apk it crashes the browser.