Hi Liam,
our apps don’t wrap the theme.liquid content, but we have found some clients with this situation, with themes such as Envy 26.4.0 or LangShop Theme 2.14.5. However, we don’t think this is a theme feature, rather it may be caused by some third app.
Anyway, we find the theme.liquid file with situations like:
{%- capture minified -%}
...
...
{%- endcapture minified -%}
where the “minified” variable is used in other templates, causing app embed blocks not being injected.
Could you try it? Thanks in advance and kind regards.