As we move toward making Site Identity activated by default, I've found that SI custom code needs to vary quite a bit depending on the theme. To accomodate this here at the theme demo site, I replaced the one-code-for-all data input in the SI configuration page with an include statement:
missing page for plugin INCLUDE
This loads a default file in /templates, the content of which used to be the data input in the config box. To make a site-wide change in the custom code, edit this file rather than changing the data input on the SI admin page.
Now there can be a sicustomcode.tpl file in a theme's template directory if that theme needs its own SI custom code. I realize this is a step backward from the no-template-editing, Web-based customization emphasis of Site Identity, but something like this is needed at a site that has SI enabled and uses and needs to accomodate multiple themes. I have more themes in the pipeline that need to specify unique SI custom code.
In future theme releases, which will all use SI, a sicustomcode.tpl file will be included. Users can either use the include statement method, or paste the content of the file into the SI custom code textarea and then edit it as they want. The tpl file will be a backup/reference in that case.