markdown scope overrides JS

[toppsdown]

Hey there, I'm new to Sublime syntax settings so apologies for my ignorance.

I'm trying to get this syntax highlighting but sublime is acting strange. The - include: scope:text.html.markdown is overriding most of the other settings.

Example:
With: - include: scope:text.html.markdown

Without: - include: scope:text.html.markdown

I tried changing the order, but then it overrides even more of the settings.

contexts:
  main:
    - include: scope:text.html.markdown
    - include: core

I've tried reading the sublime documentation but I don't see anything that describes precedence or ordering of scopes.

Thanks in advance!