You can edit the theme.tres file. First make a theme of all the types you want and their properties you want to change. Save the theme and then open it up in a text editor such as Sublime or VSCode.
Will look something like this:
[resource]
default_font = SubResource("SystemFont_hs86w")
default_font_size = 20
Button/colors/font_color = Color(1, 0, 0, 1)
Button/colors/font_disabled_color = Color(0, 1, 0, 1)
Button/colors/font_focus_color = Color(0, 0, 0, 1)
Button/colors/font_hover_color = Color(0, 0, 1, 1)
CheckBox/colors/font_color = Color(0, 0, 0, 1)
CheckBox/colors/font_disabled_color = Color(0, 0, 0, 1)
CheckBox/colors/font_focus_color = Color(0, 0, 0, 1)
CheckBox/colors/font_hover_color = Color(0, 0, 0, 1)
Then using regular expression replace all the properties of all the types to what you want
For example to make all the font_colors properties to red use this:
Replace this:
font_color = (.*)
with this:
font_color = Color(1, 0, 0, 1)
Save the file after you are done and use it in your application.